@article {pmid40036335,
year = {2025},
author = {Bergman, S and Birk, C and Holmqvist, E},
title = {ProQ prevents mRNA degradation through inhibition of poly(A) polymerase.},
journal = {Nucleic acids research},
volume = {53},
number = {5},
pages = {},
doi = {10.1093/nar/gkaf103},
pmid = {40036335},
issn = {1362-4962},
support = {2016-03656//Swedish Research Council/ ; ICA16-0021//Swedish Foundation for Strategic Research/ ; },
mesh = {*Salmonella typhimurium/genetics/pathogenicity ; *Bacterial Proteins/metabolism/genetics ; *Polynucleotide Adenylyltransferase/metabolism/genetics ; *Sigma Factor/metabolism/genetics ; *RNA Stability ; *RNA, Messenger/metabolism/genetics ; *Biofilms/growth & development ; *Gene Expression Regulation, Bacterial ; RNA-Binding Proteins/metabolism/genetics ; 3' Untranslated Regions/genetics ; Polyadenylation ; },
abstract = {The RNA-binding protein ProQ interacts with many transcripts in the bacterial cell. ProQ binding is associated with increased messenger RNA (mRNA) levels, but a mechanistic explanation for this effect has been lacking. In Salmonella Typhimurium, ProQ affects key traits associated with infection, including motility and intracellular survival. However, the direct links between ProQ activity and these phenotypes are not well understood. Here, we demonstrate that ProQ promotes biofilm formation, another virulence-associated phenotype. This effect is strictly dependent on sigma factor RpoS. ProQ increases both RpoS protein and rpoS mRNA levels, but neither affects rpoS transcription nor translation. The rpoS mRNA is a ProQ target, and expression of the rpoS 3'UTR alone is strongly dependent on ProQ. RpoS expression becomes independent of ProQ in strains lacking poly(A) polymerase I (PAPI), indicating that ProQ protects against 3' end-dependent decay. Indeed, purified ProQ inhibits PAPI-mediated polyadenylation at RNA 3' ends. Finally, PAPI is required for ProQ's effect on expression of genes involved in biofilm, motility, osmotic stress, and virulence, indicating that inhibition of polyadenylation is a general function of ProQ.},
}

*Salmonella typhimurium/genetics/pathogenicity
*Bacterial Proteins/metabolism/genetics
*Polynucleotide Adenylyltransferase/metabolism/genetics
*Sigma Factor/metabolism/genetics
*RNA Stability
*RNA, Messenger/metabolism/genetics
*Biofilms/growth & development
*Gene Expression Regulation, Bacterial
RNA-Binding Proteins/metabolism/genetics
3' Untranslated Regions/genetics
Polyadenylation

@article {pmid40035762,
year = {2025},
author = {Raymond, JA},
title = {A horizontally transferred bacterial gene aids the freezing tolerance of Antarctic bdelloid rotifers.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {10},
pages = {e2421910122},
doi = {10.1073/pnas.2421910122},
pmid = {40035762},
issn = {1091-6490},
support = {OPP-9814294//National Science Foundation (NSF)/ ; OPP-088000//National Science Foundation (NSF)/ ; },
mesh = {Antarctic Regions ; *Gene Transfer, Horizontal ; *Freezing ; Animals ; *Rotifera/genetics ; Genes, Bacterial ; Antifreeze Proteins/genetics/metabolism ; },
abstract = {Bdelloid rotifers are well known for their abilities to survive long periods of freezing as well as acquire foreign genes. Recently sequenced genomes of some bdelloid rotifers in England were found to encode several proteins similar to ice-binding proteins (IBPs) that are usually associated with freeze-thaw tolerance. Here, I describe bdelloid rotifers inhabiting an algal patch in Antarctica that have multiple homologs of these genes. Structures of the proteins predicted by AlphaFold show that they are well designed for ice-binding and a recombinant protein made for one of them showed strong ice-binding activity. The existence of multiple copies of these proteins is another characteristic of IBPs. Furthermore, multiple bdelloid rotifers in the algal patch were revived in less than an hour after storage at -25 °C for 24 y, an apparent record for laboratory-controlled studies. Several characteristics of these genes point to bacteria as their source: sequence homology, absence of introns, and a structural peculiarity so far found only in bacteria. The remarkable freezing tolerance of bdelloid rotifers can thus be at least partially attributed to horizontally acquired bacterial genes encoding IBPs.},
}

Antarctic Regions
*Gene Transfer, Horizontal
*Freezing
Animals
*Rotifera/genetics
Genes, Bacterial
Antifreeze Proteins/genetics/metabolism

@article {pmid40035521,
year = {2025},
author = {Kanakapura Sundararaj, B and Goyal, M and Samuelson, J},
title = {Targets for the diagnosis of Acanthamoeba eye infections include four cyst wall proteins and the mannose-binding domain of the trophozoite mannose-binding protein.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0094824},
doi = {10.1128/msphere.00948-24},
pmid = {40035521},
issn = {2379-5042},
abstract = {Acanthamoebae, which are free-living amoebae, cause corneal inflammation (keratitis) and blindness, if not quickly diagnosed and effectively treated. The walls of Acanthamoeba cysts contain cellulose and have two layers connected by conical ostioles. Cysts are identified by in vivo confocal microscopy of the eye or calcofluor-white- or Giemsa-labeling of corneal scrapings, both of which demand great expertise. Trophozoites, which use a mannose-binding protein to adhere to keratinocytes, are identified in eye cultures that delay diagnosis and treatment. We recently used structural and experimental methods to characterize cellulose-binding domains of Luke and Leo lectins, which are abundant in the inner layer and ostioles. However, no antibodies have been made to these lectins or to a Jonah lectin and a laccase, which are abundant in the outer layer. Here, confocal microscopy of rabbit antibodies (rAbs) to recombinant Luke, Leo, Jonah, and laccase supported localizations of GFP-tagged proteins in walls of transfected Acanthamoebae. rAbs efficiently detected calcofluor white-labeled cysts of 10 of the 11 Acanthamoeba isolates tested, including six T4 genotypes that cause most cases of keratitis. Further, laccase shed into the medium during encystation was detected by an enzyme-linked immunoassay. Structural and experimental methods identified the mannose-binding domain (ManBD) of the Acanthamoeba mannose-binding protein, while rAbs to the ManBD efficiently detected DAPI-labeled trophozoites from all 11 Acanthamoeba isolates tested. We conclude that antibodies to four cyst wall proteins and the ManBD efficiently identify Acanthamoeba cysts and trophozoites, respectively.IMPORTANCEFree-living amoeba in the soil or water cause Acanthamoeba keratitis, which is diagnosed by identification of unlabeled cysts by in vivo confocal microscopy of the eye or calcofluor-white (CFW) labeled cysts by fluorescence microscopy of corneal scrapings. Alternatively, Acanthamoeba infections are diagnosed by the identification of trophozoites in eye cultures. Here, we showed that rabbit antibodies (rAbs) to four abundant cyst wall proteins (Jonah, Luke, Leo, and laccase) each efficiently identify CFW-labeled cysts of 10 of the 11 Acanthamoeba isolates tested. Further, laccase released into the medium by encysting Acanthamoebae was detected by an enzyme-linked immunoassay. We also showed that rAbs to the mannose-binding domain (ManBD) of the Acanthamoeba mannose-binding protein, which mediates adherence of trophozoites to keratinocytes, efficiently identify DAPI-labeled trophozoites of all 11 Acanthamoeba isolates tested. In summary, four wall proteins and the ManBD appear to be excellent targets for the diagnosis of Acanthamoeba cysts and trophozoites, respectively.},
}

@article {pmid40032822,
year = {2025},
author = {Biller, SJ and Ryan, MG and Li, J and Burger, A and Eppley, JM and Hackl, T and DeLong, EF},
title = {Distinct horizontal gene transfer potential of extracellular vesicles versus viral-like particles in marine habitats.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {2126},
pmid = {40032822},
issn = {2041-1723},
support = {OCE-2049004//National Science Foundation (NSF)/ ; OCE-2304066//National Science Foundation (NSF)/ ; 917971//Simons Foundation/ ; },
mesh = {*Gene Transfer, Horizontal ; *Extracellular Vesicles/metabolism ; *Ecosystem ; Seawater/microbiology/virology ; Interspersed Repetitive Sequences ; Viruses/genetics/metabolism ; },
abstract = {Horizontal gene transfer (HGT) is enabled in part through the movement of DNA within two broad groups of small (<0.2 µm), diffusible nanoparticles: extracellular vesicles (EVs) and virus-like particles (VLPs; including viruses, gene transfer agents, and phage satellites). The information enclosed within these structures represents a substantial portion of the HGT potential available in planktonic ecosystems, but whether some genes might be preferentially transported through one type of nanoparticle versus another is unknown. Here we use long-read sequencing to compare the genetic content of EVs and VLPs from the oligotrophic North Pacific. Fractionated EV-enriched and VLP-enriched subpopulations contain diverse DNA from the surrounding microbial community, but differ in their capacity and encoded functions. The sequences carried by both particle types are enriched in mobile genetic elements (MGEs) as compared with other cellular chromosomal regions, and we highlight how this property enables novel MGE discovery. Examining the Pelagibacter mobilome reveals >7200 distinct chromosomal fragments and MGEs, many differentially partitioned between EVs and VLPs. Together these results suggest that distinctions in nanoparticle contents contribute to the mode and trajectory of microbial HGT networks and evolutionary dynamics in natural habitats.},
}

*Gene Transfer, Horizontal
*Extracellular Vesicles/metabolism
*Ecosystem
Seawater/microbiology/virology
Interspersed Repetitive Sequences
Viruses/genetics/metabolism

@article {pmid40032228,
year = {2025},
author = {Jiang, Z and Zeng, J and Wang, X and Yu, H and Yue, L and Wang, C and Chen, F and Wang, Z},
title = {Biodegradable microplastics and dissemination of antibiotic resistance genes: an undeniable risk associated with plastic additives.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {125952},
doi = {10.1016/j.envpol.2025.125952},
pmid = {40032228},
issn = {1873-6424},
abstract = {Biodegradable plastics (BDPs) represent a promising alternative to conventional plastics; however, the release of microplastics (MPs) during degradation necessitates an urgent investigation into their biological effects. The potential risks associated with MPs and additives released from BDPs, particularly in facilitating the dissemination of antibiotic resistance genes (ARGs), remain largely unknown. This study aims to investigate the effects of polylactic acid (PLA) MPs and their common plasticizer, dibutyl phthalate (DBP), on the horizontal gene transfer (HGT) of ARGs using conjugative transfer and transformation model systems. The viability of Escherichia coli (E. coli) cells after exposure to PLA MPs (0.01, 0.1, 1, and 10 mg L[-1]), DBP (0.01, 0.1, 1, and 10 μg L[-1]) alone, or in combination (1 mg L[-1] PLA MPs + 1 μg L[-1]DBP) remained unaffected. Exposure to PLA MPs at environmentally relevant concentrations did not promote the HGT of ARGs. However, the addition of DBP significantly enhanced the transfer frequency by 1.5-1.8 folds compared to exposure to PLA MPs alone. The accelerated dissemination of ARGs was primarily attributed to the elevated levels of reactive oxygen species (by 26.2%), increased membrane permeability (by 19.4%), and the up-regulation of genes involved in mating pair formation (by 1.6-3.8 folds) and DNA translocation (by 1.5-3.4 folds). These findings underscore the critical role of additives and highlight the potential accumulative effects associated with prolonged exposure to high concentrations of PLA MPs, which should be considered for a comprehensive risk assessment of BDPs.},
}

@article {pmid40029705,
year = {2025},
author = {Hong, J and Xue, W and Wang, T},
title = {Emergence of alternative stable states in microbial communities undergoing horizontal gene transfer.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
pmid = {40029705},
issn = {2050-084X},
support = {12401660//National Natural Science Foundation of China/ ; HSE499011086//Shenzhen Institue of Synthetic Biology Scientific Research Program/ ; },
mesh = {*Gene Transfer, Horizontal ; *Microbiota/genetics ; Bacteria/genetics ; Models, Theoretical ; Microbial Interactions/genetics ; Interspersed Repetitive Sequences/genetics ; Ecosystem ; },
abstract = {Microbial communities living in the same environment often display alternative stable states, each characterized by a unique composition of species. Understanding the origin and determinants of microbiome multistability has broad implications in environments, human health, and microbiome engineering. However, despite its conceptual importance, how multistability emerges in complex communities remains largely unknown. Here, we focused on the role of horizontal gene transfer (HGT), one important aspect mostly overlooked in previous studies, on the stability landscape of microbial populations. Combining mathematical modeling and numerical simulations, we demonstrate that, when mobile genetic elements (MGEs) only affect bacterial growth rates, increasing HGT rate in general promotes multistability of complex microbiota. We further extend our analysis to scenarios where HGT changes interspecies interactions, microbial communities are subjected to strong environmental selections and microbes live in metacommunities consisting of multiple local habitats. We also discuss the role of different mechanisms, including interspecies interaction strength, the growth rate effects of MGEs, MGE epistasis and microbial death rates in shaping the multistability of microbial communities undergoing HGT. These results reveal how different dynamic processes collectively shape community multistability and diversity. Our results provide key insights for the predictive control and engineering of complex microbiota.},
}

*Gene Transfer, Horizontal
*Microbiota/genetics
Bacteria/genetics
Models, Theoretical
Microbial Interactions/genetics
Interspersed Repetitive Sequences/genetics
Ecosystem

@article {pmid40027803,
year = {2025},
author = {Christman, ND and Dalia, AB},
title = {The molecular basis for DNA-binding by competence T4P is distinct in Gram-positive and Gram-negative species.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.17.638644},
pmid = {40027803},
issn = {2692-8205},
abstract = {UNLABELLED: Competence type IV pili (T4P) are bacterial surface appendages that facilitate DNA uptake during horizontal gene transfer by natural transformation. These dynamic structures actively extend from the cell surface, bind to DNA in the environment, and then retract to import bound DNA into the cell. Competence T4P are found in diverse Gram-negative (diderm) and Gram-positive (monoderm) bacterial species. While the mechanism of DNA-binding by diderm competence T4P has been the recent focus of intensive study, relatively little is known about DNA-binding by monoderm competence T4P. Here, we use Streptococcus pneumoniae as a model system to address this question. Competence T4P likely bind to DNA via a tip-associated complex of proteins called minor pilins, and recent work highlights a high degree of structural conservation between the minor pilin tip complexes of monoderm and diderm competence T4P. In diderms, positively charged residues in one minor pilin, FimT, are critical for DNA-binding. We show that while these residues are conserved in ComGD, the FimT homolog of monoderms, they only play a minor role in DNA uptake for natural transformation. Instead, we find that two-positively charged residues in the neighboring minor pilin, ComGF (the PilW homolog of monoderms), play the dominant role in DNA uptake for natural transformation. Furthermore, we find that these residues are conserved in other monoderms, but not diderms. Together, these results suggest that the molecular basis for DNA-binding has either diverged or evolved independently in monoderm and diderm competence T4P.

AUTHOR SUMMARY: Diverse bacteria use extracellular structures called competence type IV pili (T4P) to take up DNA from their environment. The uptake of DNA by T4P is the first step of natural transformation, a mode of horizontal gene transfer that contributes to the spread of antibiotic resistance and virulence traits in diverse clinically relevant Gram-negative (diderm) and Gram-positive (monoderm) bacterial species. While the mechanism of DNA binding by competence T4P in diderms has been an area of recent study, relatively little is known about how monoderm competence T4P bind DNA. Here, we explore how monoderm competence T4P bind DNA using Streptococcus pneumoniae as a model system. Our results indicate that while monoderm T4P and diderm T4P likely have conserved structural features, the DNA-binding mechanism of each system is distinct.},
}

@article {pmid40027742,
year = {2025},
author = {Tabatabaee, Y and Zhang, C and Arasti, S and Mirarab, S},
title = {Species tree branch length estimation despite incomplete lineage sorting, duplication, and loss.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.20.639320},
pmid = {40027742},
issn = {2692-8205},
abstract = {UNLABELLED: Phylogenetic branch lengths are essential for many analyses, such as estimating divergence times, analyzing rate changes, and studying adaptation. However, true gene tree heterogeneity due to incomplete lineage sorting (ILS), gene duplication and loss (GDL), and horizontal gene transfer (HGT) can complicate the estimation of species tree branch lengths. While several tools exist for estimating the topology of a species tree addressing various causes of gene tree discordance, much less attention has been paid to branch length estimation on multi-locus datasets. For single-copy gene trees, some methods are available that summarize gene tree branch lengths onto a species tree, including coalescent-based methods that account for heterogeneity due to ILS. However, no such branch length estimation method exists for multi-copy gene family trees that have evolved with gene duplication and loss. To address this gap, we introduce the CASTLES-Pro algorithm for estimating species tree branch lengths while accounting for both GDL and ILS. CASTLES-Pro improves on the existing coalescent-based branch length estimation method CASTLES by increasing its accuracy for single-copy gene trees and extends it to handle multi-copy ones. Our simulation studies show that CASTLES-Pro is generally more accurate than alternatives, eliminating the systematic bias toward overestimating terminal branch lengths often observed when using concatenation. Moreover, while not theoretically designed for HGT, we show that CASTLES-Pro maintains relatively high accuracy under high rates of random HGT.

CODE AVAILABILITY: CASTLES-Pro is implemented inside the software package ASTER, available at https://github.com/chaoszhang/ASTER .

DATA AVAILABILITY: The datasets and scripts used in this study are available at https://github.com/ytabatabaee/CASTLES-Pro-paper .},
}

@article {pmid40027631,
year = {2025},
author = {Schmidt, H and Raphael, BJ},
title = {The tree labeling polytope: a unified approach to ancestral reconstruction problems.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.14.638328},
pmid = {40027631},
issn = {2692-8205},
abstract = {MOTIVATION: Reconstructing unobserved ancestral states of a phylogenetic tree provides insight into the history of evolving systems and is one of the fundamental problems in phylogenetics. For a fixed phylogenetic tree, the most parsimonious ancestral reconstruction - a solution to the small parsimony problem - can be efficiently found using the dynamic programming algorithms of Fitch-Hartigan and Sankoff. Ancestral reconstruction is important in many applications including inferring the routes of metastases in cancer, deriving the transmission history of viruses, determining the direction of cellular differentiation in organismal development, and detecting recombination and horizontal gene transfer in phylogenetic networks. However, most of these applications impose additional global constraints on the reconstructed ancestral states, which break the local structure required in the recurrences of Fitch-Hartigan and Sankoff.

RESULTS: We introduce an alternative, polyhedral approach to ancestral reconstruction problems using the tree labeling polytope , a geometric object whose vertices represent the feasible ancestral labelings of a tree. This framework yields a polynomial-time linear programming algorithm for the small parsimony problem . More importantly, the tree labeling polytope facilitates the incorporation of additional constraints that arise in modern ancestral reconstruction problems. We demonstrate the utility of our approach by deriving mixed-integer programming algorithms with a small number of integer variables and strong linear relaxations for three such problems: the parsimonious migration history problem, the softwired small parsimony problem on phylogenetic networks, and the convex recoloring problem on trees. Our algorithms outperform existing state-of-the-art methods on both simulated and real datasets. For instance, our algorithm scales to trace routes of cancer metastases in trees with thousands of leaves, enabling the analysis of large trees generated by recent single-cell sequencing technologies. On a mouse model of metastatic lung adenocarcinoma, the tree labeling polytope allows us to infer simpler migration histories compared to previous results.

AVAILABILITY: Python implementations of the algorithms provided in this work are available at: github.com/raphael-group/tree-labeling-polytope .},
}

@article {pmid40024690,
year = {2025},
author = {Wajima, T and Tanaka, E and Uchiya, KI},
title = {Unique and Ingenious Mechanisms Underlying Antimicrobial Resistance and Spread of Haemophilus influenzae.},
journal = {Biological & pharmaceutical bulletin},
volume = {48},
number = {3},
pages = {205-212},
doi = {10.1248/bpb.b23-00640},
pmid = {40024690},
issn = {1347-5215},
mesh = {*Haemophilus influenzae/drug effects ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Haemophilus Infections/drug therapy/microbiology ; *Drug Resistance, Bacterial/genetics ; Animals ; },
abstract = {Antimicrobial resistance (AMR) is a serious global concern. AMR pathogens are found in hospitals and communities. Haemophilus influenzae is a common pathogen associated with community-acquired infections. H. influenzae infections are usually treated with β-lactams, macrolides, and quinolones. However, the drug-resistant strains have emerged. The resistance mechanisms of H. influenzae are complex but are roughly characterized by the acquisition of a mutation in antimicrobial-targeting genes and exogenous resistant genes. Generally, the former cannot be transferred horizontally to a susceptible strain. However, several studies have demonstrated that, in the case of H. influenzae, both the former and the latter can be transferred horizontally. In this review, we provide an overview of the bacterial features and antimicrobial resistance of H. influenzae. We also summarize the unique and ingenious antimicrobial resistance mechanisms used by this pathogen based on the findings of recent studies. These are expected to facilitate the understanding of AMR pathogens in the community and develop strategies to combat infections.},
}

*Haemophilus influenzae/drug effects
Humans
*Anti-Bacterial Agents/pharmacology
*Haemophilus Infections/drug therapy/microbiology
*Drug Resistance, Bacterial/genetics
Animals

@article {pmid40023817,
year = {2025},
author = {Shao, Y and Chen, M and Cai, J and Doi, Y and Chen, M and Wang, M and Zeng, M and Guo, Q},
title = {Cefotaxime-Resistant Neisseria meningitidis Sequence Type 4821 Causing Fulminant Meningitis.},
journal = {Emerging infectious diseases},
volume = {31},
number = {3},
pages = {591-595},
doi = {10.3201/eid3103.241493},
pmid = {40023817},
issn = {1080-6059},
mesh = {Humans ; *Cefotaxime/therapeutic use/pharmacology ; *Neisseria meningitidis/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Child, Preschool ; *Meningitis, Meningococcal/microbiology/drug therapy ; Microbial Sensitivity Tests ; China ; Male ; Drug Resistance, Bacterial ; },
abstract = {We explored the role of commensal Neisseria in the emergence of third-generation cephalosporin-resistant N. meningitidis. Cefotaxime resistance-conferring penA795 was prevalent among commensal Neisseria isolates in Shanghai, China, and was acquired by a serogroup C quinolone-resistant sequence type 4821 N. meningitidis, Nm507, causing fulminant meningitis in an unvaccinated 2-year-old child.},
}

Humans
*Cefotaxime/therapeutic use/pharmacology
*Neisseria meningitidis/genetics/drug effects
*Anti-Bacterial Agents/pharmacology/therapeutic use
Child, Preschool
*Meningitis, Meningococcal/microbiology/drug therapy
Microbial Sensitivity Tests
China
Male
Drug Resistance, Bacterial

@article {pmid40019366,
year = {2025},
author = {Hu, Y and Gong, C and Yang, Z and Han, H and Tian, T and Yang, X and Xie, W and Wang, S and Wu, Q and Zhou, X and Turlings, TCJ and Guo, Z and Zhang, Y},
title = {Functional Divergence of Plant-Derived Thaumatin-Like Protein Genes in Two Closely Related Whitefly Species.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2502193},
doi = {10.1002/advs.202502193},
pmid = {40019366},
issn = {2198-3844},
support = {2021YFD1400600//National Key R & D Program of China/ ; GZB20240839//Postdoctoral Fellowship Program of CPSF/ ; Y2023XK15//Central Public-interest Scientific Institution Basal Research Fund/ ; Y2024XK01//Central Public-interest Scientific Institution Basal Research Fund/ ; //Beijing Key Laboratory for Pest Control and Sustainable Cultivation of Vegetables/ ; //Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences/ ; 788949//European Research Council Advanced/ ; CARS-23//Earmarked Fund for China Agriculture Research System/ ; 2024M753572//China Postdoctoral Science Foundation/ ; 32221004//National Natural Science Foundation of China/ ; },
abstract = {The recent discovery that various insects have acquired functional genes through horizontal gene transfer (HGT) has prompted numerous studies into this puzzling and fascinating phenomenon. So far, horizontally transferred genes are found to be functionally conserved and largely retained their ancestral functions. It evidently has not yet been considered that horizontally transferred genes may evolve and can contribute to divergence between species. Here, it is first showed that the genomes of the two widespread and agriculturally important whiteflies Trialeurodes vaporariorum and Bemisia tabaci both contain a plant-derived thaumatin-like protein (TLP) gene, but with highly distinct functions in these closely related pests. In T. vaporariorum, TLP has maintained a function similar to that of the plant donor, acting as an antimicrobial protein to resist fungal infection; but in sharp contrast, in B. tabaci, TLP has evolved into an effector that suppresses plant defense responses. These findings reveal an as-yet undescribed scenario of cross-species functional differentiation of horizontally transferred genes and suggest that the HGT-mediated evolutionary novelty can contribute to ecotypic divergence and even speciation.},
}

@article {pmid40013789,
year = {2025},
author = {Jin, M and Rouxel, O and Quintin, N and Geslin, C},
title = {Molecular piracy in deep-sea hydrothermal vent: phage-plasmid interactions revealed by phage-FISH in Marinitoga piezophila.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0230624},
doi = {10.1128/aem.02306-24},
pmid = {40013789},
issn = {1098-5336},
abstract = {UNLABELLED: Prokaryotes and mobile genetic elements (MGEs, such as viruses and plasmids) interact extensively, leading to horizontal gene transfer (HGT) and consequent microbial evolution and diversity. However, our knowledge of the interactions between MGEs in deep-sea hydrothermal ecosystems is limited. In this study, we adapted a phage-fluorescence in situ hybridization (phage-FISH) approach to visualize and quantify the dynamics of phage-plasmid interactions in an anaerobic, thermophilic deep-sea bacterium, Marinitoga piezophila. Notably, our results revealed that plasmid signals were detected in viral particles released from lysed cells, indicating that mitomycin C not only induced plasmid replication but also its packaging into phage particles. Further analysis of the DNA content in purified virions showed that the phage capsids incorporated plasmid DNA even without induction, and the majority of capsids (up to 70%) preferentially packaged plasmid DNA rather than viral DNA after induction. Therefore, this study provided direct evidence of molecular piracy in the deep-sea hydrothermal ecosystem, highlighting the important roles of selfish MGEs in virus-host interactions and HGT in extreme marine environments.

IMPORTANCE: Deep-sea hydrothermal vents are hotspots for microbes. Several studies revealed that virus-mediated horizontal gene transfer (HGT) in deep-sea hydrothermal vent ecosystems may be crucial to the survival and stability of prokaryotes in these extreme environments. However, little is known about the interaction between viruses and other mobile genetic elements (MGEs, such as plasmids), and how their interactions influence virus-mediated HGT in these ecosystems. In this study, we adapted a phage-fluorescence in situ hybridization approach to directly monitor the dynamics of phage-plasmid-host interactions at the single-cell level in the Marinitoga piezophila model. Interestingly, our results indicate that plasmid DNA could not only be induced by mitomycin C to a great extent but also hijacked viral assembly machinery to facilitate its propagation and spread. Therefore, the data presented here imply that the interaction between the viruses and other MGEs could play profound roles in virus-host interaction and virus-mediated HGT in the deep-sea hydrothermal ecosystem.},
}

@article {pmid40012781,
year = {2025},
author = {Zhao, B and Zhang, R and Jin, B and Yu, Z and Wen, W and Zhao, T and Quan, Y and Zhou, J},
title = {Sludge water: a potential pathway for the spread of antibiotic resistance and pathogenic bacteria from hospitals to the environment.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1492128},
pmid = {40012781},
issn = {1664-302X},
abstract = {Hospitals play an important role in the spread of antibiotic resistance genes (ARGs) and antimicrobial resistance (AMR). The ARGs present in hospital wastewater tend to accumulate in activated sludge, with different ARGs exhibiting varying migration rates. As a result, sludge water produced during the activated sludge treatment process may be a significant source of ARGs entering the environment. Despite this, research into the behavior of ARGs during sludge concentration and dewatering remains limited. This study hypothesizes that ARGs might exhibit new behaviors in sludge water during sludge concentration. Using metagenomic analysis, we explored the distribution and migration risks of ARGs and human pathogenic bacteria (HPB) in sludge water, comparing them with those in hospital wastewater. The findings reveal a strong correlation between ARGs in sludge water and hospital wastewater, with subtypes such as arlR, efpA, and tetR showing higher abundance in sludge water. Although the horizontal gene transfer potential of ARGs is greater in hospital wastewater than in sludge water, the resistance mechanisms and migration pathways are similar even when their HPB host associations differ. ARGs in both environments are primarily transmitted through coexisting mobile genetic elements (MGEs). This suggests that sludge water serves as a critical route for the release of hospital-derived ARGs into the environment, posing potential threats to public health and ecological safety.},
}

@article {pmid39898629,
year = {2025},
author = {Huang, S and Wei, DD and Hong, H and Chen, S and Fan, L-P and Huang, Q-S and Du, F-L and Xiang, T-X and Li, P and Zhang, W and Wan, L-G and Liu, Y},
title = {Capture of mobile genetic elements following intercellular conjugation promotes the production of ST11-KL64 CR-hvKP.},
journal = {Microbiology spectrum},
volume = {13},
number = {3},
pages = {e0134724},
doi = {10.1128/spectrum.01347-24},
pmid = {39898629},
issn = {2165-0497},
support = {82102411, 32370195, 82260403//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Klebsiella pneumoniae/genetics/pathogenicity/metabolism ; *Klebsiella Infections/microbiology ; *Conjugation, Genetic ; *Plasmids/genetics ; Humans ; *Interspersed Repetitive Sequences ; Virulence/genetics ; Gene Transfer, Horizontal ; Animals ; Whole Genome Sequencing ; Mice ; Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; Carbapenem-Resistant Enterobacteriaceae/genetics/isolation & purification ; },
abstract = {UNLABELLED: Sequence type (ST)11 carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) can cause life-threatening infections and is therefore of global concern. Despite its importance, the evolutionary history and mechanism for the emergence of ST11 CR-hvKP are unclear. In recent years, the detection rate of ST11 CR-hvKP has increased in a teaching hospital. Based on its clonal transmission, a conjugation experiment was performed between a hvKP strain AP8555 and a ST11 CRKP strain, resulting in two ST11 CR-hvKP strains. Research had confirmed that the virulence plasmid pAP855 was horizontally transferred to the CRKP strain to form the conjugant S270-Tc, which was recombined by mobile genetic elements to evolve into the conjugant S270-Tc-R. The S270-Tc-R had high virulence, high plasmid stability, and greater adaptability. Interestingly, it had high homology to clinically prevalent ST11 CR-hvKP strains using pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing (WGS). This is the first demonstration that plasmid recombination in vitro has led to the formation of ST11 CR-hvKP strains. The clinical setting is a multi-factorial and multi-selection pressure environment that may stimulate the evolution of conjugant strains in the transition period to local strains in the stable period, and surveillance is urgently needed for infection control.

IMPORTANCE: The emergence of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) heralded the onset of a new and rapidly worsening public health disaster on a global scale. More attention has been paid to its evolutionary history and mechanism, which currently remains unclear. In this study, a conjugation experiment was performed between a hvKP strain AP8555 and a ST11 CRKP strain, resulting in two ST11 CR-hvKP strains. We had confirmed that the virulence plasmid pAP855 was horizontally transferred to the CRKP strain to form the conjugant S270-Tc, which was recombined by mobile genetic elements to evolve into the conjugant S270-Tc-R. The S270-Tc-R had high virulence, high plasmid stability, and greater adaptability. Interestingly, it had high homology to clinically prevalent ST11 CR-hvKP strains using pulsed-field gel electrophoresis and whole-genome sequencing.},
}

*Klebsiella pneumoniae/genetics/pathogenicity/metabolism
*Klebsiella Infections/microbiology
*Conjugation, Genetic
*Plasmids/genetics
Humans
*Interspersed Repetitive Sequences
Virulence/genetics
Gene Transfer, Horizontal
Animals
Whole Genome Sequencing
Mice
Anti-Bacterial Agents/pharmacology
Carbapenems/pharmacology
Carbapenem-Resistant Enterobacteriaceae/genetics/isolation & purification

@article {pmid40010677,
year = {2025},
author = {Lapadula, WJ and Cañadas, MG and Ayub, MJ},
title = {Characterization of Ribosome inactivating protein genes and their transcripts in Trialeurodes vaporariorum.},
journal = {Gene},
volume = {948},
number = {},
pages = {149356},
doi = {10.1016/j.gene.2025.149356},
pmid = {40010677},
issn = {1879-0038},
abstract = {Ribosome-inactivating proteins (RIPs) are rRNA N-glycosylases (EC 3.2.2.22) that depurinate an adenine residue from the conserved alpha-sarcin/ricin loop in rRNA, blocking protein synthesis. In previous research, we demonstrated that whiteflies from the Aleyrodidae family (e.g., Bemisia tabaci), mosquitoes from the Culicinae subfamily (e.g., Aedes aegypti), and flies of Sciaroidea superfamily (e.g., Contarinia nasturtii) acquired these genes via three independent horizontal gene transfer events. The temporal expression profiles analyzed in mosquitoes and flies are consistent with the expected for immune effector molecules of insects. Notably, in A. aegypti, we found that these genes contribute to immunity. In whiteflies, codon analysis suggests that RIP genes have evolved under the influence of natural selection. Public transcriptomic experiments have shown that these genes are expressed in the adult stage of B. tabaci. Despite computational findings supporting RIP genes functionality in whiteflies, no experimental studies have been conducted. Furthermore, there is currently no publicly available RNA-seq data evaluating gene expression throughout ontogeny in the Aleyrodidae family. In this work, we experimentally demonstrated the presence of these foreign genes in the genome of Trialeurodes vaporariorum. We quantified their expression across the life cycle stages of this species and analyzed their untranslated regions. The results obtained contribute to a deeper understanding of the biological roles that these ribotoxin encoding genes may play in whiteflies and other insects.},
}

@article {pmid40010597,
year = {2025},
author = {Wang, X and Lin, Y and Li, S and Wang, J and Li, X and Zhang, D and Duan, D and Shao, Z},
title = {Metagenomic analysis reveals the composition and sources of antibiotic resistance genes in coastal water ecosystems of the Yellow Sea and Yangtze River Delta.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {371},
number = {},
pages = {125923},
doi = {10.1016/j.envpol.2025.125923},
pmid = {40010597},
issn = {1873-6424},
abstract = {The rapid development of coastal areas has raised concerns about marine environmental pollution. In this study, metagenomics was employed to investigate antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and bacterial communities in the Yellow Sea and Yangtze River Delta in China. Multidrug resistance genes were the most abundant ARGs in these regions. Transposons and insertion_element_IS91 were the dominant MGEs, closely related to the horizontal gene transfer of ARGs. Temperature, dissolved oxygen, pH, and depth were identified as important environmental factors influencing the distribution of ARGs in seawater. Oil, agriculture, animal husbandry, and wastewater treatment plants are likely the primary sources of ARGs. From the perspective of ARG control, bacterial communities contributed the most to the development of the resistome and may carry ARGs, spreading from the Yangtze River Delta to the Yellow Sea along ocean currents. A comparison with Tara Oceans datasets revealed that the dominant ARG types and bacterial genera in coastal waters were consistent with global characteristics, with variations in ARG subtypes. This study expands knowledge on the distribution patterns of ARGs at an offshore scale and provides a reference for the prevention and control of resistant gene pollution in the Yellow Sea and Yangtze River Delta.},
}

@article {pmid40008406,
year = {2025},
author = {Heida, A and Hamilton, MT and Gambino, J and Sanderson, K and Schoen, ME and Jahne, MA and Garland, J and Ramirez, L and Quon, H and Lopatkin, AJ and Hamilton, KA},
title = {Population Ecology-Quantitative Microbial Risk Assessment (QMRA) Model for Antibiotic-Resistant and Susceptible E. coli in Recreational Water.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c07248},
pmid = {40008406},
issn = {1520-5851},
abstract = {Understanding and predicting the role of waterborne environments in transmitting antimicrobial-resistant (AMR) infections are critical for public health. A population ecology-quantitative microbial risk assessment (QMRA) model is proposed to evaluate urinary tract infection (UTI) development due to recreational waterborne exposures to Escherichia coli (E. coli) and antibiotic-resistant extended-spectrum β-lactamase-producing (ESBL) E. coli. The horizontal gene transfer (HGT) mechanism of conjugation and other evolutionary factors were modeled separately in the environment and the gut. Persistence/dilution dominated HGT in the environment; however, HGT highly impacted predicted ESBL populations in the body. Predicted disability life year (DALY) risks from exposure to ESBL E. coli at concentrations consistent with US recreational water criteria were less than the 10[-6] pppy benchmark value but greater than the susceptible E. coli DALY risks associated with a UTI health outcome. However, the prevailing susceptible dose-response relationship may underestimate ESBL risk if HGT rates in vivo approach those reported in vitro. A sensitivity analysis demonstrated that DALY values, E. coli/ESBL concentrations, and exposure parameters were influential on predicted risks. The model is a preliminary tool to begin the expansion of the QMRA paradigm to explore the impacts of evolutionary changes in AMR risk assessment.},
}

@article {pmid40007369,
year = {2025},
author = {Li, S and Liu, Y and Zhang, Y and Huang, P and Bartlam, M and Wang, Y},
title = {Stereoselective behavior of naproxen chiral enantiomers in promoting horizontal transfer of antibiotic resistance genes.},
journal = {Journal of hazardous materials},
volume = {489},
number = {},
pages = {137692},
doi = {10.1016/j.jhazmat.2025.137692},
pmid = {40007369},
issn = {1873-3336},
abstract = {Antibiotic resistance poses a global threat to public health, with recent studies highlighting the role of non-antibiotic pharmaceuticals in the transmission of antibiotic resistance genes (ARGs). This study provides insights into the comprehensive profile, horizontal gene transfer potential, hosts, and public health risks associated with antibiotic resistomes in river ecosystems exposed to chiral naproxen (NAP). Our findings demonstrate that NAP stress selectively enriches ARGs and mobile genetic elements (MGEs), thereby bolstering bacterial resistance to specific antibiotics. Importantly, the spatial variation of NAP chiral enantiomers influences the enantioselective response of bacterial communities to antibiotics. While (S)-NAP and (R)-NAP exhibit differing degrees of horizontal transfer potential, (S/R)-NAP notably facilitates microbial aggregation and DNA transport via type IV secretion system (T4SS)-related functional genes, promoting the conjugation of sul1. Moreover, (S/R)-NAP promotes the horizontal transfer of ARGs by stimulating ROS production and altering cell membrane permeability. Chiral NAP exposure induces pathogens to acquire ARGs and accelerates the proliferation of Burkholderia. ARG-Rank analysis indicates that the health risk posed by (R)-NAP exposure surpasses that of (S)-NAP, with the highest risk observed when both enantiomers are present. This study elucidates the horizontal transfer and transmission mechanisms of ARGs under chiral NAP stress, underscoring the potential health hazards associated with NAP chiral enantiomers.},
}

@article {pmid40007158,
year = {2025},
author = {Ma, S and Li, S and Lu, X and Zhang, Q and Dong, M and Wu, Y and Lv, D and Luo, L and Jin, W and Liu, X and Yang, W and Djalovic, I and Wang, T and Zhou, X and Chen, R},
title = {A transposon-based cargo system mediates gene trafficking and creates ultra-clean transgenic plants after stable transformation.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70017},
pmid = {40007158},
issn = {1469-8137},
support = {2023ZD0403005//Biological Breeding-Major Projects/ ; 32171453//National Natural Science Foundation of China/ ; 20220101//CAAS-Syngenta Innovation Expansion Project/ ; 2021YFD1200700//National Key Research and Development Program of China/ ; //Innovation Program of Chinese Academy of Agricultural Sciences/ ; },
abstract = {Genetically modified crops have profound impacts on cost savings and environmental friendliness conferred by new traits, such as resistance to insects and herbicides. Selectable marker genes are essential for screening transformed cells, but they are undesirable in the final product due to the risks of horizontal gene transfer and extensive safety assessment requirements. Generating marker- and backbone-free lines can enhance the public acceptance of transgenic crops. Here, we established a transposon-mediated ultra-clean selectable transformant (TRUST) system for generating marker- and backbone-free transformants in a visibly controllable manner, facilitated by the integration of transposon elements, fluorescence proteins, and the anthocyanin biosynthesis gene. This system creates ultra-clean transgenic events that retain only the expression cassette of the gene of interest with an average probability of 15.5%. Additionally, long-read whole-genome sequencing confirmed the integrity of the expression cassette boundaries. The TRUST system is not only a powerful method for producing backbone-free transgenic plants but also increases the number of transgenic events originating from one starting event, thereby potentially leading to advances in the genetic engineering of recalcitrant crop varieties.},
}

@article {pmid39980242,
year = {2025},
author = {Yonemitsu, MA and Sevigny, JK and Vandepas, LE and Dimond, JL and Giersch, RM and Gurney-Smith, HJ and Abbott, CL and Supernault, J and Withler, R and Smith, PD and Weinandt, SA and Garrett, FES and Child, ZJ and Sigo, RLW and Unsell, E and Crim, RN and Metzger, MJ},
title = {Multiple Lineages of Transmissible Neoplasia in the Basket Cockle (C. nuttallii) With Repeated Horizontal Transfer of Mitochondrial DNA.},
journal = {Molecular ecology},
volume = {34},
number = {6},
pages = {e17682},
doi = {10.1111/mec.17682},
pmid = {39980242},
issn = {1365-294X},
support = {//National Research Council/ ; 2208081//Division of Ocean Sciences/ ; A19AP00215//Bureau of Indian Affairs/ ; },
mesh = {Animals ; *DNA, Mitochondrial/genetics ; *Cardiidae/genetics ; *Phylogeny ; *Gene Transfer, Horizontal ; Neoplasms/genetics ; Washington ; },
abstract = {Transmissible cancers are clonal lineages of neoplastic cells able to infect multiple hosts, spreading through populations in the environment as an infectious disease. Transmissible cancers have been identified in Tasmanian devils, dogs, and bivalves. Several lineages of bivalve transmissible neoplasias (BTN) have been identified in multiple bivalve species. In 2019 in Puget Sound, Washington, USA, disseminated neoplasia was observed in basket cockles (Clinocardium nuttallii), a species that is important to the culture and diet of the Suquamish Tribe as well as other tribes with traditional access to the species. To test whether disseminated neoplasia in cockles is a previously unknown lineage of BTN, a nuclear locus was amplified from cockles from Agate Pass, Washington, and sequences revealed evidence of transmissible cancer in several individuals. We used a combination of cytology and quantitative PCR to screen collections of cockles from 11 locations in Puget Sound and along the Washington coastline to identify the extent of contagious cancer spread in this species. Two BTN lineages were identified in these cockles, with one of those lineages (CnuBTN1) being the most prevalent and geographically widespread. Within the CnuBTN1 lineage, multiple nuclear loci support the conclusion that all cancer samples form a single clonal lineage. However, the mitochondrial alleles in each cockle with CnuBTN1 are different from each other, suggesting mitochondrial genomes of this cancer have been replaced multiple times during its evolution, through horizontal transmission. The identification and analysis of these BTNs are critical for broodstock selection, management practices, and repopulation of declining cockle populations, which will enable continued cultural connection and dietary use of the cockles by Coast Salish Tribes.},
}

Animals
*DNA, Mitochondrial/genetics
*Cardiidae/genetics
*Phylogeny
*Gene Transfer, Horizontal
Neoplasms/genetics
Washington

@article {pmid39599474,
year = {2024},
author = {McDonald, NL and Wareham, DW and Bean, DC},
title = {Aeromonas and mcr-3: A Critical Juncture for Transferable Polymyxin Resistance in Gram-Negative Bacteria.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {11},
pages = {},
pmid = {39599474},
issn = {2076-0817},
mesh = {*Aeromonas/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; Humans ; *Polymyxins/pharmacology ; *Gram-Negative Bacterial Infections/microbiology/drug therapy ; *Colistin/pharmacology ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; Gram-Negative Bacteria/drug effects/genetics ; Phylogeny ; Drug Resistance, Multiple, Bacterial/genetics ; Bacterial Proteins/genetics ; Gene Transfer, Horizontal ; Escherichia coli Proteins/genetics ; Transferases (Other Substituted Phosphate Groups) ; },
abstract = {Polymyxin antibiotics B and colistin are considered drugs of last resort for the treatment of multi-drug and carbapenem-resistant Gram-negative bacteria. With the emergence and dissemination of multi-drug resistance, monitoring the use and resistance to polymyxins imparted by mobilised colistin resistance genes (mcr) is becoming increasingly important. The Aeromonas genus is widely disseminated throughout the environment and serves as a reservoir of mcr-3, posing a significant risk for the spread of resistance to polymyxins. Recent phylogenetic studies and the identification of insertion elements associated with mcr-3 support the notion that Aeromonas spp. may be the evolutionary origin of the resistance gene. Furthermore, mcr-3-related genes have been shown to impart resistance in naïve E. coli and can increase the polymyxin MIC by up to 64-fold (with an MIC of 64 mg/L) in members of Aeromonas spp. This review will describe the genetic background of the mcr gene, the epidemiology of mcr-positive isolates, and the relationship between intrinsic and transferable mcr resistance genes, focusing on mcr-3 and mcr-3-related genes.},
}

*Aeromonas/genetics/drug effects
*Anti-Bacterial Agents/pharmacology
Humans
*Polymyxins/pharmacology
*Gram-Negative Bacterial Infections/microbiology/drug therapy
*Colistin/pharmacology
Drug Resistance, Bacterial/genetics
Microbial Sensitivity Tests
Gram-Negative Bacteria/drug effects/genetics
Phylogeny
Drug Resistance, Multiple, Bacterial/genetics
Bacterial Proteins/genetics
Gene Transfer, Horizontal
Escherichia coli Proteins/genetics
Transferases (Other Substituted Phosphate Groups)

@article {pmid40005743,
year = {2025},
author = {Liu, F and Cheewangkoon, R and Zhao, RL},
title = {Discovery of a New Starship Transposon Driving the Horizontal Transfer of the ToxA Virulence Gene in Alternaria ventricosa.},
journal = {Microorganisms},
volume = {13},
number = {2},
pages = {},
pmid = {40005743},
issn = {2076-2607},
support = {(Project ID: 31961143010,31970010,32300012)//National Natural Science Foundation of China/ ; },
abstract = {The virulence gene ToxA has been proposed to be horizontally transferred between three fungal wheat pathogens (Parastagonospora nodorum, Pyrenophora tritici-repentis, and Bipolaris sorokiniana) as part of a conserved ~14 kb ToxhAT transposon. Here, our analysis of 2137 fungal species-representative assemblies revealed that the ToxA gene is an isolate of Alternaria ventricosa and shows a remarkable 99.5% similarity to those found in B. sorokiniana and P. tritici-repentis. Analysis of the regions flanking ToxA within A. ventricosa revealed that it was embedded within a 14 kb genomic element nearly identical to the corresponding ToxhAT regions in B. sorokiniana, P. nodorum, and P. tritici-repentis. Comparative analysis further showed that ToxhAT in A. ventricosa resides within a larger mobile genetic element, which we identified as a member of the Starship transposon superfamily, named Frontier. Our analysis demonstrated that ToxhAT has been independently captured by three distinct Starships-Frontier, Sanctuary, and Horizon-which, despite having minimal sequence similarity outside of ToxhAT, facilitate its mobilization. These findings place Frontier, Sanctuary, and Horizon within a growing class of Starships implicated in the horizontal transfer of adaptive genes among fungal species. Moreover, we identified three distinct HGT events involving ToxA across these four fungal species, reinforcing the hypothesis of a single evolutionary origin for the ToxhAT transposon. These findings underscore the pivotal role of transposon-mediated HGT in the adaptive evolution of eukaryotic pathogens, offering new insights into how transposons facilitate genetic exchange and shape host-pathogen interactions in fungi.},
}

@article {pmid38895396,
year = {2025},
author = {Chang, TH and Pourtois, JD and Haddock, NL and Furkuawa, D and Kelly, KE and Amanatullah, DF and Burgener, E and Milla, C and Banaei, N and Bollyky, PL},
title = {Prophages are Infrequently Associated With Antibiotic Resistance in Pseudomonas aeruginosa Clinical Isolates.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.06.02.595912},
pmid = {38895396},
issn = {2692-8205},
support = {R01 HL148184/HL/NHLBI NIH HHS/United States ; },
abstract = {UNLABELLED: Lysogenic bacteriophages can integrate their genome into the bacterial chromosome in the form of a prophage and can promote genetic transfer between bacterial strains in vitro . However, the contribution of lysogenic phages to the incidence of antimicrobial resistance (AMR) in clinical settings is poorly understood. Here, in a set of 186 clinical isolates of Pseudomonas aeruginosa collected from respiratory cultures from 82 patients with cystic fibrosis (CF), we evaluate the links between prophage counts and both genomic and phenotypic resistance to six anti-pseudomonal antibiotics: tobramycin, colistin, ciprofloxacin, meropenem, aztreonam, and piperacillin-tazobactam. We identified 239 different prophages in total. We find that P. aeruginosa isolates contain on average 3.06 +/- 1.84 (SD) predicted prophages. We find no significant association between the number of prophages per isolate and the minimum inhibitory concentration (MIC) for any of these antibiotics. We then investigate the relationship between particular prophages and AMR. We identify a single lysogenic phage associated with phenotypic resistance to the antibiotic tobramycin and, consistent with this association, we observe that AMR genes associated with resistance to tobramycin are more likely to be found when this prophage is present. However we find that they are not encoded directly on prophage sequences. Additionally, we identify a single prophage statistically associated with ciprofloxacin resistance but do not identify any genes associated with ciprofloxacin phenotypic resistance. These findings suggest that prophages are only infrequently associated with the AMR genes in clinical isolates of P. aeruginosa .

IMPORTANCE: Antibiotic-resistant infections of Pseudomonas aeruginosa , a leading pathogen in patients with Cystic Fibrosis (CF) are a global health threat. While lysogenic bacteriophages are known to facilitate horizontal gene transfer, their role in promoting antibiotic resistance in clinical settings remains poorly understood. In our analysis of 186 clinical isolates of P. aeruginosa from CF patients, we find that prophage abundance does not predict phenotypic resistance to key antibiotics but that specific prophages are infrequently associated with tobramycin resistance genes. In addition, we do not find antimicrobial resistance (AMR) genes encoded directly on prophages. These results highlight that while phages can be associated with AMR, phage-mediated AMR transfer may be rare in clinical isolates and difficult to identify. This work is important for future efforts on mitigating AMR in Cystic Fibrosis and other vulnerable populations affected by Pseudomonas aeruginosa infections and advances our understanding of bacterial-phage dynamics in clinical infections.},
}

@article {pmid40001581,
year = {2025},
author = {Liu, Z and Fan, X and Wu, Y and Zhang, W and Zhang, X and Xu, D and Wang, Y and Sun, K and Wang, W and Ye, N},
title = {Comparative Genomics of Bryopsis hypnoides: Structural Conservation and Gene Transfer Between Chloroplast and Mitochondrial Genomes.},
journal = {Biomolecules},
volume = {15},
number = {2},
pages = {},
pmid = {40001581},
issn = {2218-273X},
mesh = {*Genome, Mitochondrial/genetics ; *Genome, Chloroplast/genetics ; *Phylogeny ; *Genomics/methods ; Codon Usage ; Evolution, Molecular ; Gene Transfer, Horizontal ; RNA, Transfer/genetics ; },
abstract = {Bryopsis hypnoides, a unicellular multinucleate green alga in the genus Bryopsis, plays vital ecological roles and represents a key evolutionary link between unicellular and multicellular algae. However, its weak genetic baseline data have constrained the progress of evolutionary research. In this study, we successfully assembled and annotated the complete circular chloroplast and mitochondrial genomes of B. hypnoides. The chloroplast genome has a total length of 139,745 bp and contains 59 protein-coding genes, 2 rRNA genes, and 11 tRNA genes, with 31 genes associated with photosynthesis. The mitochondrial genome has a total length of 408,555 bp and contains 41 protein-coding genes, 3 rRNA genes, and 18 tRNA genes, with 18 genes involved in oxidative phosphorylation. Based on the data, we conducted a genetic comparison involving repeat sequences, phylogenetic relationships, codon usage preferences, and gene transfer between the two organellar genomes. The major results highlighted that (1) the chloroplast genome favors A/T repeats, whereas the mitochondrial genome prefers C/G repeats; (2) codon usage preference analysis indicated that both organellar genomes prefer codons ending in A/T, with a stronger bias observed in the chloroplast genome; and (3) sixteen fragments with high sequence identity were identified between the two organellar genomes, indicating potential gene transfer. These findings provide critical insights into the organellar genome characteristics and evolution of B. hypnoides.},
}

*Genome, Mitochondrial/genetics
*Genome, Chloroplast/genetics
*Phylogeny
*Genomics/methods
Codon Usage
Evolution, Molecular
Gene Transfer, Horizontal
RNA, Transfer/genetics

@article {pmid40001396,
year = {2025},
author = {Sher, AA and Whitehead-Tillery, CE and Peer, AM and Bell, JA and Vocelle, DB and Dippel, JT and Zhang, L and Mansfield, LS},
title = {Dynamic Spread of Antibiotic Resistance Determinants by Conjugation to a Human-Derived Gut Microbiota in a Transplanted Mouse Model.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {2},
pages = {},
pmid = {40001396},
issn = {2079-6382},
support = {RN031097-DEHN//Albert C. and Lois E. Dehn Chair Endowment/ ; NC1202//United States Department of Agriculture/ ; GS100019//University Distinguished Professor Endowment, Michigan State University/ ; U19AI090872//National Institutes of Health, Enterics Research Investigational Network, Cooperative Research Center/ ; Stipend to Azam A. Sher//College of Veterinary Medicine/ ; },
abstract = {BACKGROUND: Antibiotic-resistant (AR) bacteria pose an increasing threat to public health, but the dynamics of antibiotic resistance gene (ARG) spread in complex microbial communities are poorly understood. Conjugation is a predominant direct cell-to-cell mechanism for the horizontal gene transfer (HGT) of ARGs. We hypothesized that commensal Escherichia coli donor strains would mediate the conjugative transfer of ARGs to phylogenetically distinct bacteria without antibiotic selection pressure in gastrointestinal tracts of mice carrying a human-derived microbiota with undetectable levels of E. coli. Our objective was to identify a mouse model to study the factors regulating AR transfer by conjugation in the gut.

METHODS: Two donor E. coli strains were engineered to carry chromosomally encoded red fluorescent protein, and an ARG- and green fluorescent protein (GFP)-encoding broad host range RP4 conjugative plasmid. Mice were orally gavaged with two donor strains (1) E. coli MG1655 or (2) human-derived mouse-adapted E. coli LM715-1 and their colonization assessed by culture over time. Fluorescence-activated cell sorting (FACS) and 16S rDNA sequencing were performed to trace plasmid spread to the microbiota.

RESULTS: E. coli LM715-1 colonized mice for ten days, while E. coli MG1655 was not recovered after 72 h. Bacterial cells from fecal samples on days 1 and 3 post inoculation were sorted by FACS. Samples from mice given donor E. coli LM715-1 showed an increase in cells expressing green but not red fluorescence compared to pre-inoculation samples. 16S rRNA gene sequencing analysis of FACS GFP positive cells showed that bacterial families Lachnospiraceae, Clostridiaceae, Pseudomonadaceae, Rhodanobacteraceae, Erysipelotrichaceae, Oscillospiraceae, and Butyricicoccaceae were the primary recipients of the RP4 plasmid.

CONCLUSIONS: Results show this ARG-bearing conjugative RP4 plasmid spread to diverse human gut bacterial taxa within a live animal where they persisted. These fluorescent marker strategies and human-derived microbiota transplanted mice provided a tractable model for investigating the dynamic spread of ARGs within gut microbiota and could be applied rigorously to varied microbiotas to understand conditions facilitating their spread.},
}

@article {pmid40001389,
year = {2025},
author = {Pandova, M and Kizheva, Y and Hristova, P},
title = {Relationship Between CRISPR-Cas Systems and Acquisition of Tetracycline Resistance in Non-Clinical Enterococcus Populations in Bulgaria.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {2},
pages = {},
pmid = {40001389},
issn = {2079-6382},
support = {project No BG-RRP-2.004-0008//European Union-NextGenerationEU, National Recovery and Resilience Plan of the Republic of Bulgaria, SUMMIT 3.2.4./ ; },
abstract = {Non-clinical enterococci are relatively poorly studied by means of acquired antibiotic resistance to tetracycline and by the distribution, functionality and role of their CRISPR systems. Background: In our study, 72 enterococcal strains, isolated from various non-clinical origins, were investigated for their phenotypic and genotypic (tet(M), tet(O), tet(S), tet(L), tet(K), tet(T) and tet(W)) tetracycline resistance. Methods: The genetic determinants for HGT (MGEs (Int-Tn and prgW), inducible pheromones (cpd, cop and cff), aggregation substances (agg, asa1, prgB and asa373) and CRISPR-Cas systems were characterized by PCR and whole-genome sequencing. Results: Four tet genes (tetM, tetO, tetS and tetT) were detected in 39% (n = 28) of our enterococcal population, with tetM (31%) being dominant. The gene location was linked to the Tn6009 transposon. All strains that contained tet genes also had genes for HGT. No tet genes were found in E. casseliflavus and E. gilvus. In our study, 79% of all tet-positive strains correlated with non-functional CRISPR systems. The strain E. faecalis BM15 was the only one containing a combination of a functional CRISPR system (cas1, cas2, csn2 and csn1/cas9) and tet genes. The CRISPR subtype repeats II-A, III-B, IV-A2 and VI-B1 were identified among E. faecalis strains (CM4-II-A, III-B and VI-B1; BM5-IV-A2, II-A and III-B; BM12 and BM15-II-A). The subtype II-A was the most present. These repeats enclosed a great number of spacers (1-10 spacers) with lengths of 31 to 36 bp. One CRISPR locus was identified in plasmid (p.Firmicutes1 in strain E. faecalis BM5). We described the presence of CRISPR loci in the species E. pseudoavium, E. pallens and E. devriesei and their lack in E. gilvus, E. malodoratus and E. mundtii. Conclusions: Our findings generally describe the acquisition of foreign DNA as a consequence of CRISPR inactivation, and self-targeting spacers as the main cause.},
}

@article {pmid40001375,
year = {2025},
author = {La Rosa, MC and Maugeri, A and Favara, G and La Mastra, C and Magnano San Lio, R and Barchitta, M and Agodi, A},
title = {The Impact of Wastewater on Antimicrobial Resistance: A Scoping Review of Transmission Pathways and Contributing Factors.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {2},
pages = {},
pmid = {40001375},
issn = {2079-6382},
abstract = {BACKGROUND/OBJECTIVES: Antimicrobial resistance (AMR) is a global issue driven by the overuse of antibiotics in healthcare, agriculture, and veterinary settings. Wastewater and treatment plants (WWTPs) act as reservoirs for antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs). The One Health approach emphasizes the interconnectedness of human, animal, and environmental health in addressing AMR. This scoping review analyzes wastewater's role in the AMR spread, identifies influencing factors, and highlights research gaps to guide interventions.

METHODS: This scoping review followed the PRISMA-ScR guidelines. A comprehensive literature search was conducted across the PubMed and Web of Science databases for articles published up to June 2024, supplemented by manual reference checks. The review focused on wastewater as a source of AMR, including hospital effluents, industrial and urban sewage, and agricultural runoff. Screening and selection were independently performed by two reviewers, with conflicts resolved by a third.

RESULTS: Of 3367 studies identified, 70 met the inclusion criteria. The findings indicated that antibiotic residues, heavy metals, and microbial interactions in wastewater are key drivers of AMR development. Although WWTPs aim to reduce contaminants, they often create conditions conducive to horizontal gene transfer, amplifying resistance. Promising interventions, such as advanced treatment methods and regulatory measures, exist but require further research and implementation.

CONCLUSIONS: Wastewater plays a pivotal role in AMR dissemination. Targeted interventions in wastewater management are essential to mitigate AMR risks. Future studies should prioritize understanding AMR dynamics in wastewater ecosystems and evaluating scalable mitigation strategies to support global health efforts.},
}

@article {pmid40000989,
year = {2025},
author = {Zhao, M and Zhang, Y and Liu, S and Wang, F and Zhang, P},
title = {Eradication of Helicobacter pylori reshapes gut microbiota and facilitates the evolution of antimicrobial resistance through gene transfer and genomic mutations in the gut.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {90},
pmid = {40000989},
issn = {1471-2180},
support = {32201393//National Natural Science Foundation of China/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; Humans ; *Helicobacter pylori/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; *Helicobacter Infections/microbiology/drug therapy ; *Gene Transfer, Horizontal ; *Feces/microbiology ; Mutation ; Metagenomics ; Klebsiella/genetics/drug effects ; Female ; Male ; Genome, Bacterial/genetics ; Adult ; Escherichia/genetics/drug effects ; Middle Aged ; Genes, Bacterial/genetics ; },
abstract = {Treating Helicobacter pylori (H. pylori) infection requires large quantities of antibiotics, thus dramatically promoting the enrichment and dissemination of antimicrobial resistance (AMR) in feces. However, the influence of H. pylori eradication on the AMR mobility and the gut microbiota evolution has yet to be thoroughly investigated. Here, a study involving 12 H. pylori-positive participants was conducted, and the pre- and post- eradication fecal samples were sequenced. Metagenomic analysis revealed that the eradication treatment drastically altered the gut microbiome, with the Escherichia and Klebsiella genera emerging as the predominant bacteria. Interestingly, the eradication treatment significantly increased the relative abundance and diversity of resistome and mobilome in gut microbiota. Eradication of H. pylori also enriched AMR genes (ARGs) conferring resistance to antibiotics not administered because of the co-location with other ARGs or mobile genetic elements (MGEs). Additionally, the Escherichia and Klebsiella genera were identified as the primary bacterial hosts of these highly transferable ARGs. Furthermore, the genomic variations associated with ARGs in Escherichia coli (E. coli) caused by the eradication treatment were profiled, including the parC, parE, and gyrA genes. These findings revealed that H. pylori eradication promoted the enrichment of ARGs and MGEs in the Escherichia and Klebsiella genera, and further facilitated bacterial evolution through the horizontal transfer of ARGs and genomic variations.},
}

*Gastrointestinal Microbiome/drug effects/genetics
Humans
*Helicobacter pylori/genetics/drug effects
*Drug Resistance, Bacterial/genetics
*Anti-Bacterial Agents/pharmacology
*Helicobacter Infections/microbiology/drug therapy
*Gene Transfer, Horizontal
*Feces/microbiology
Mutation
Metagenomics
Klebsiella/genetics/drug effects
Female
Male
Genome, Bacterial/genetics
Adult
Escherichia/genetics/drug effects
Middle Aged
Genes, Bacterial/genetics

@article {pmid39998220,
year = {2025},
author = {Kwak, Y and Argandona, JA and Miao, S and Son, TJ and Hansen, AK},
title = {A dual insect symbiont and plant pathogen improves insect host fitness under arginine limitation.},
journal = {mBio},
volume = {},
number = {},
pages = {e0358824},
doi = {10.1128/mbio.03588-24},
pmid = {39998220},
issn = {2150-7511},
abstract = {Some facultative bacterial symbionts are known to benefit insects, but nutritional advantages are rare among these non-obligate symbionts. Here, we demonstrate that the facultative symbiont Candidatus Liberibacter psyllaurous enhances the fitness of its psyllid insect host, Bactericera cockerelli, by providing nutritional benefits. L. psyllaurous, an unculturable pathogen of solanaceous crops, also establishes a close relationship with its insect vector, B. cockerelli, increasing in titer during insect development, vertically transmitting through eggs, and colonizing various tissues, including the bacteriome, which houses the obligate nutritional symbiont, Carsonella. Carsonella supplies essential amino acids to its insect host but has gaps in some of its essential amino acid pathways that the psyllid complements with its own genes, many of which have been acquired through horizontal gene transfer (HGT) from bacteria. Our findings reveal that L. psyllaurous increases psyllid fitness on plants by reducing developmental time and increasing adult weight. In addition, through metagenomic sequencing, we reveal that L. psyllaurous maintains complete pathways for synthesizing the essential amino acids arginine, lysine, and threonine, unlike the psyllid's other resident microbiota, Carsonella, and two co-occurring Wolbachia strains. RNA sequencing reveals the downregulation of a HGT collaborative psyllid gene (ASL), which indicates a reduced demand for arginine supplied by Carsonella when the psyllid is infected with L. psyllaurous. Notably, artificial diet assays show that L. psyllaurous enhances psyllid fitness on an arginine-deplete diet. These results corroborate the role of L. psyllaurous as a beneficial insect symbiont, contributing to the nutrition of its insect host.IMPORTANCEUnlike obligate symbionts that are permanently associated with their hosts, facultative symbionts rarely show direct nutritional contributions, especially under nutrient-limited conditions. This study demonstrates, for the first time, that Candidatus Liberibacter psyllaurous, a facultative symbiont and a plant pathogen, enhances the fitness of its Bactericera cockerelli host by supplying an essential nutrient arginine that is lacking in the plant sap diet. Our findings reveal how facultative symbionts can play a vital role in helping their insect hosts adapt to nutrient-limited environments. This work provides new insights into the dynamic interactions between insect hosts, their symbiotic microbes, and their shared ecological niches, broadening our understanding of symbiosis and its role in shaping adaptation and survival.},
}

@article {pmid39993662,
year = {2025},
author = {Chen, M and Yan, X and Tang, Q and Liu, M and Yang, M and Chai, Y and Wei, Y and Shen, P and Zhang, J},
title = {Particle size transfer of antibiotic resistance genes in typical processes of municipal wastewater treatment plant.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132288},
doi = {10.1016/j.biortech.2025.132288},
pmid = {39993662},
issn = {1873-2976},
abstract = {Occurrence and transfer of antibiotic resistance genes (ARGs) was investigated concerning sludge particle size in a typical wastewater treatment plant, and the roles of vertical (VGT) and horizontal gene transfer (HGT) in the spread of ARGs were explored. Results showed that although membrane bioreactor (MBR) effectively reduced the relative abundance of ARGs, it concurrently enriched ARGs in MBR sludge, particularly for the largest-size particle sludge (>150 μm). A decreasing trend in the relative abundance of ARGs was observed along with the decreasing sludge particle size, and larger particle sludge (>106 μm) formed a relatively stable composition of ARGs, while ARGs on smaller particle sludge (6.5-106 μm) fluctuate rapidly. Particle size does not affect the abundance distribution patterns or assembly mechanisms of ARGs as deterministic processes. The smallest-size particles were the primary attachment site for bacterial pathogens. Larger-size particle sludge (>106 μm) showed higher HGT frequency with Proteobacteria as the dominant hosts undergoing HGT.},
}

@article {pmid39990427,
year = {2025},
author = {Cai, L and Havird, JC and Jansen, RK},
title = {Recombination and retroprocessing in broomrapes reveal a universal roadmap for mitochondrial evolution in heterotrophic plants.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.14.637881},
pmid = {39990427},
issn = {2692-8205},
abstract = {The altered life history strategies of heterotrophic organisms often leave a profound genetic footprint on energy metabolism related functions. In parasitic plants, the reliance on host-derived nutrients and loss of photosynthesis in holoparasites have led to highly degraded to absent plastid genomes, but its impact on mitochondrial genome (mitogenome) evolution has remained controversial. By examining mitogenomes from 45 Orobanchaceae species including three independent transitions to holoparasitism and key evolutionary intermediates, we identified measurable and predictable genetic alterations in genomic shuffling, RNA editing, and intracellular (IGT) and horizontal gene transfer (HGT) en route to a nonphotosynthetic lifestyle. In-depth comparative analyses revealed DNA recombination and repair processes, especially RNA-mediated retroprocessing, as significant drivers for genome structure evolution. In particular, we identified a novel RNA-mediated IGT and HGT mechanism, which has not been demonstrated in cross-species and inter-organelle transfers. Based on this, we propose a generalized dosage effect mechanism to explain the biased transferability of plastid DNA to mitochondria across green plants, especially in heterotrophic lineages like parasites and mycoheterotrophs. Evolutionary rates scaled with these genomic changes, but the direction and strength of selection varied substantially among genes and clades, resulting in high contingency in mitochondrial genome evolution. Finally, we describe a universal roadmap for mitochondrial evolution in heterotrophic plants where increased recombination and repair activities, rather than relaxed selection alone, lead to differentiated genome structure compared to free-living species.},
}

@article {pmid39988254,
year = {2025},
author = {Hou, W and Yu, J and Shi, H and Xu, J and Chen, SS and Shaban, SS and Kim, Y and Bai, J},
title = {As a reservoir of antibiotic resistance genes and pathogens, the hydrodynamic characteristics drive their distribution patterns in Lake Victoria.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {370},
number = {},
pages = {125903},
doi = {10.1016/j.envpol.2025.125903},
pmid = {39988254},
issn = {1873-6424},
abstract = {Antibiotic resistance genes (ARGs) and pathogenic bacteria pose significant challenges to human health, and hydrodynamic processes complicate their transmission mechanisms in lake ecosystems, particularly in tropical regions. Lake Victoria supports abundant water resources and provides livelihoods for millions of people, yet the environmental behavior of ARGs and pathogenic bacteria remains unclear. Herein, the novel insights into the co-occurrence patterns and transmission mechanisms of ARGs and pathogenic bacteria in Lake Victoria was investigated via molecular techniques and a hydrodynamic model. The results showed that as a large reservoir of ARGs and pathogenic bacteria, a total of 172 ARG subtypes and 93 pathogenic bacteria were identified in Lake Victoria. ARGs were spread through mobile genetic elements (tnpA4 and int2), enhancing the antibiotic resistance and virulence factors (secretion systems, regulatory factors, and toxins) of various pathogenic bacteria. The hydrodynamic model indicated that surface wind-driven currents and bottom compensatory flows shaped the outward dispersion of ARGs and pathogenic bacteria from the gulf. The NCM model suggested that water exchange accelerated the diffusion of antibiotics and pathogens, likely enhancing the deterministic assembly process of ARGs and the stochastic assembly process of pathogens. The PLS-PM model revealed that hydrodynamics directly influenced the accumulation of ARGs and pathogenic bacteria, and subsequently affected the diffusion and distribution patterns of ARGs and pathogens by facilitating the propagation of MGEs. Our study overcomes the limitations associated with lake and microenvironmental scale, providing insights and understanding into the transmission mechanisms of ARGs and pathogenic bacteria.},
}

@article {pmid39988071,
year = {2025},
author = {Le, NT and Hoang, PH and Nguyen, Q and Truong, MNH and Van Dang, C and Ho, TH and Hoang, PL and Truong, DQ and Nguyen, HTT and Van Le, C and Phan, TTP},
title = {Emergence of mcr-8.2-mediated colistin resistance in Klebsiella pneumoniae isolated from pediatric diarrhea cases in southern Vietnam.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2025.02.007},
pmid = {39988071},
issn = {2213-7173},
abstract = {BACKGROUND: Colistin resistance poses a growing global challenge, particularly in low- and middle-income countries where antibiotic misuse is prevalent. This study investigates the prevalence of colistin resistance in Klebsiella spp. and characterizes the genetic features of resistant isolates, focusing on the mcr-8.2 gene identified in a Klebsiella pneumoniae isolate from pediatric diarrheal cases in southern Vietnam.

METHODS: Stool samples were collected from 500 pediatric patients (aged 0-5 years) hospitalized with diarrhea in two tertiary hospitals in Ho Chi Minh City between March and September 2022. Samples were cultured on Violet Red Bile Glucose Agar, then presumptive Klebsiella spp. colonies were selected, purified on nutrient agar, and identified using MALDI-TOF MS. Colistin resistance was determined via minimum inhibitory concentration testing, and the presence of mcr genes was confirmed through polymerase chain reaction. Whole-genome sequencing was performed on the Klebsiella pneumoniae strain harboring mcr-8.2 to elucidate resistance mechanisms. Strain characterization was performed using multi-locus sequence typing, while conjugation experiments assessed horizontal gene transfer potential.

RESULTS: Among 121 Klebsiella spp. isolates, 49 (40.5%) were resistant to colistin. The mcr-1 gene was detected in 31 isolates (25.6%), whereas the mcr-8 was identified in a single isolate (0.8%), with a colistin MIC of 16 µg/mL. Genomic analysis revealed 34 antibiotic resistance genes, including mcr-8.2 and multiple β-lactamase genes, alongside plasmid types IncFIB and IncFII. Chromosomal mutations in phoP, phoQ, and lpxM were also implicated in colistin resistance.

CONCLUSIONS: This study documents the emergence of mcr-8.2-mediated colistin resistance in K. pneumoniae from pediatric diarrhea in Vietnam and highlights a high prevalence of multidrug resistance in Klebsiella spp.. Continuous surveillance of mcr genes and novel therapeutic strategies are urgently needed.},
}

@article {pmid39987875,
year = {2025},
author = {Pourrostami Niavol, K and Andaluri, G and Achary, MP and Suri, RPS},
title = {How does carbon to nitrogen ratio and carrier type affect moving bed biofilm reactor (MBBR): Performance evaluation and the fate of antibiotic resistance genes.},
journal = {Journal of environmental management},
volume = {377},
number = {},
pages = {124619},
doi = {10.1016/j.jenvman.2025.124619},
pmid = {39987875},
issn = {1095-8630},
abstract = {With the spread of antibiotic resistance genes (ARGs) in the environment, monitoring and controlling ARGs have become an emerging issue of concern in biological processes. Moving bed biofilm reactors (MBBR) have been gaining attention for application in wastewater treatment. Since the performance of MBBR depends on operational parameters and biocarriers, selection of suitable biocarriers and start-up conditions are vital for efficiency of MBBRs. This study investigates the effects of different carbon-to-nitrogen (C/N) ratios and carrier types on the fate of selected ARGs and microbial communities in four MBBR systems using two conventional (K3 and sponge biocarrier (SB)) and two modified carriers (Fe-Ca@SB and Ze-AC@SB). Results showed that the modified biocarriers achieved higher NH4-N removal and better simultaneous nitrification and denitrification (SND) performance (90%) at C/N of 20. However, as the C/N ratio decreased to 10 and 7, the performance of all bioreactors was approximately similar. Moreover, COD removal of 90% was achieved in all reactors regardless of C/N ratio and carrier type. Further studies on the fate of selected ARGs (tetA, blaTEM, ampR) showed that the C/N ratio could affect the abundance of target ARGs, especially for K3 biocarrier, with tetA being the most abundant gene. Also, as the C/N ratio decreased, intl1 was enriched using K3 and SB. However, for Ze-AC@SB, the increase in the abundance of ARGs and intl1 was the lowest making it a reliable carrier not only in MBBR performance but in the control of ARGs. Metagenomic studies showed that the C/N ratio and carrier type could alter the diversity and structure of the bacterial communities in different MBBR systems, with Proteobacteria being the most abundant phylum in all four systems.},
}

@article {pmid39987738,
year = {2025},
author = {Su, H and Xu, W and Hu, X and Xu, Y and Wen, G and Cao, Y},
title = {The impact of microplastics on antibiotic resistance genes, metal resistance genes, and bacterial community in aquaculture environment.},
journal = {Journal of hazardous materials},
volume = {489},
number = {},
pages = {137704},
doi = {10.1016/j.jhazmat.2025.137704},
pmid = {39987738},
issn = {1873-3336},
abstract = {Microplastics are emerging contaminants. However, their effects on antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and the structure and abundance of bacterial communities, particularly pathogens, in aquaculture environments remains poorly understood. Therefore, this study investigated the effect of microplastics of different sizes on the abundance and distribution of ARGs, MRGs, and bacterial communities in aquaculture environments. The results revealed that, compared with pond water, large microplastics harbored significantly higher ARG abundances, particularly for multidrug-resistant genes; notably, level-I- and -II-risk ARGs were more prevalent on microplastics, highlighting the potential for horizontal gene transfer. Microplastics also exhibited a propensity to aggregate pathogenic bacteria such as Brucella and Pseudomonas, which could pose direct risks to aquatic product safety and public health. Network and differential network analyses revealed significant correlations between bacterial genera and ARG/MRG abundance, particularly on microplastics. Therefore, our findings suggest that microplastics act as vectors for the spread of ARGs, MRGs, and pathogens in aquaculture, potentially leading to the formation of complexes of these materials that threaten ecosystem health and human well-being. This study provides critical insights into the need for targeted management strategies to mitigate microplastic pollution in aquaculture settings.},
}

@article {pmid39981300,
year = {2025},
author = {Proença, M and Tanoeiro, L and Fox, JG and Vale, FF},
title = {Prophage dynamics in gastric and enterohepatic environments: unraveling ecological barriers and adaptive transitions.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf017},
pmid = {39981300},
issn = {2730-6151},
abstract = {Phage predation plays a critical role in shaping bacterial genetic diversity, with prophages playing a comparable role. However, the prevalence and genetic variability of prophages within the Helicobacter genus remain inadequately studied. Helicobacter species are clinically significant and occupy distinct digestive system regions, with gastric species (e.g. Helicobacter pylori) residing in the gastric mucosa and enterohepatic species colonizing the liver and intestines of various vertebrates. Here, we address this knowledge gap by analyzing prophage presence and diversity across 343 non-pylori Helicobacter genomes, mapping their distribution, comparing genomic features between gastric and enterohepatic prophages, and exploring their evolutionary relationships with hosts. We identified and analyzed a catalog of 119 new complete and 78 incomplete prophages. Our analysis reveals significant differences between gastric and enterohepatic species. Gastric prophages exhibit high synteny, and cluster in a few groups, indicating a more conserved genetic structure. In contrast, enterohepatic prophages show greater diversity in gene order and content, reflecting their adaptation to varied host environments. Helicobacter cinaedi stands out, harboring a large number of prophages among the enterohepatic species, forming a distinct cohesive group. Phylogenetic analyses reveal a co-evolutionary relationship between several prophages and their bacterial hosts-though exceptions, such as the enterohepatic prophages from H. canis, H. equorum, H. jaachi, and the gastric prophage from H. himalayensis-suggesting more complex co-evolutionary dynamics like host jumps, recombination, and horizontal gene transfer. The insights gained from this study enhance our understanding of prophage dynamics in Helicobacter, emphasizing their role in bacterial adaptation, virulence, and host specificity.},
}

@article {pmid39979200,
year = {2025},
author = {Huisman, JS and Bernhard, A and Igler, C},
title = {Should I stay or should I go: transmission trade-offs in phages and plasmids.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.01.007},
pmid = {39979200},
issn = {1878-4380},
abstract = {Mobile genetic elements (MGEs), like temperate bacteriophages and conjugative plasmids, are major vectors of virulence and antibiotic resistance in bacterial populations. For reproductive success, MGEs must balance horizontal and vertical transmission. Yet, the cost of horizontal transmission (metabolic burden or host death) puts these transmission modes at odds. Using virulence-transmission trade-off (VTT) theory, we identify three groups of environmental variables affecting the balance between horizontal and vertical transmission: host density, host physiology, and competitors. We find that general theoretical predictions of the optimal response to environmental cues align with experimental evidence on the regulation of transmission by phages and plasmids. We further highlight gaps between theory and experiments, differences between phages and plasmids, and suggest areas for future research.},
}

@article {pmid39976625,
year = {2025},
author = {Lin, YJ and Chen, CH and Chang, IY and Chiang, RL and Wang, HY and Chiu, CH and Chen, YM},
title = {Genomic and transcriptomic insights into the virulence and adaptation of shock syndrome-causing Streptococcus anginosus.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {2},
pages = {},
doi = {10.1099/mic.0.001535},
pmid = {39976625},
issn = {1465-2080},
mesh = {*Streptococcus anginosus/genetics/pathogenicity ; *Genome, Bacterial ; Humans ; Virulence/genetics ; *Genomic Islands/genetics ; *Streptococcal Infections/microbiology ; Virulence Factors/genetics/metabolism ; Transcriptome ; Shock, Septic/microbiology ; Genomics ; Prophages/genetics ; Adolescent ; Gene Transfer, Horizontal ; Clustered Regularly Interspaced Short Palindromic Repeats ; Bacterial Proteins/genetics/metabolism ; Quorum Sensing/genetics ; },
abstract = {Streptococcus anginosus is a common isolate of the oral cavity and an opportunistic pathogen for systemic infections. Although the pyogenic infections caused by S. anginosus are similar to those caused by Streptococcus pyogenes, S. anginosus lacks most of the well-characterized virulence factors of S. pyogenes. To investigate the pathogenicity of S. anginosus, we analysed the genome of a newly identified S. anginosus strain, KH1, which was associated with toxic shock-like syndrome in an immunocompetent adolescent. The genome of KH1 contains nine genomic islands, two Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated systems and many phage-related proteins, indicating that the genome is influenced by prophages and horizontal gene transfer. Comparative genome analysis of 355 S. anginosus strains revealed a significant difference between the sizes of the pan genome and core genome, reflecting notable strain variations. We further analysed the transcriptomes of KH1 under conditions mimicking either the oral cavity or the bloodstream. We found that in an artificial saliva medium, the expression of a putative quorum quenching system and pyruvate oxidase for H2O2 production was upregulated, which could optimize the competitiveness of S. anginosus in the oral ecosystem. Conversely, in a modified serum medium, purine and glucan biosynthesis, competence and bacteriocin production were significantly upregulated, likely facilitating the survival of KH1 in the bloodstream. These findings indicate that S. anginosus can utilize diverse mechanisms to adapt to different environmental niches and establish infection, despite its lack of toxin production.},
}

*Streptococcus anginosus/genetics/pathogenicity
*Genome, Bacterial
Humans
Virulence/genetics
*Genomic Islands/genetics
*Streptococcal Infections/microbiology
Virulence Factors/genetics/metabolism
Transcriptome
Shock, Septic/microbiology
Genomics
Prophages/genetics
Adolescent
Gene Transfer, Horizontal
Clustered Regularly Interspaced Short Palindromic Repeats
Bacterial Proteins/genetics/metabolism
Quorum Sensing/genetics

@article {pmid39976429,
year = {2025},
author = {Smith, EP and Valdivia, RH},
title = {Chlamydia trachomatis: a model for intracellular bacterial parasitism.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0036124},
doi = {10.1128/jb.00361-24},
pmid = {39976429},
issn = {1098-5530},
abstract = {Chlamydia comprises a diverse group of obligate intracellular bacteria that cause infections in animals, including humans. These organisms share fascinating biology, including distinct developmental stages, non-canonical cell surface structures, and adaptations to intracellular parasitism. Chlamydia trachomatis is of particular interest due to its significant clinical importance, causing both ocular and sexually transmitted infections. The strain L2/434/Bu, responsible for lymphogranuloma venereum, is the most common strain used to study chlamydial molecular and cell biology because it grows readily in cell culture and is amenable to genetic manipulation. Indeed, this strain has enabled researchers to tackle fundamental questions about the molecular mechanisms underlying Chlamydia's developmental transitions and biphasic lifecycle and cellular adaptations to obligate intracellular parasitism, including characterizing numerous conserved virulence genes and defining immune responses. However, L2/434/Bu is not representative of C. trachomatis strains that cause urogenital infections in humans, limiting its utility in addressing questions of host tropism and immune evasion in reproductive organs. Recent research efforts are shifting toward understanding the unique attributes of more clinically relevant C. trachomatis genovars.},
}

@article {pmid39975115,
year = {2025},
author = {Bean, EL and Smith, JL and Grossman, AD},
title = {Identification of insertion sites for the integrative and conjugative element Tn9 16 in the Bacillus subtilis chromosome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39975115},
issn = {2692-8205},
abstract = {Integrative and conjugative elements (ICEs) are found in many bacterial species and are mediators of horizontal gene transfer. Tn 916 is an ICE found in several Gram-positive genera, including Enterococcus , Staphylococcus , Streptococcus , and Clostridum . In contrast to the many ICEs that preferentially integrate into a single site, Tn 916 can integrate into many sites in the host chromosome. The consensus integration motif for Tn 916 , based on analyses of approximately 200 independent insertions, is an approximately 16 bp AT-rich sequence. Here, we describe the identification and mapping of approximately 10 [5] independent Tn 916 insertions in the Bacillus subtilis chromosome. The insertions were distributed between 1,554 chromosomal sites, and approximately 99% of the insertions were in 303 sites and 65% were in only ten sites. One region, between ykuC and ykyB (kre), was a 'hotspot' for integration with ∼22% of the insertions in that single location. In almost all of the top 99% of sites, Tn 916 was found with similar frequencies in both orientations relative to the chromosome and relative to the direction of transcription, with a few notable exceptions. Using the sequences of all insertion regions, we determined a consensus motif which is similar to that previously identified for Clostridium difficile . The insertion sites are largely AT-rich, and some sites overlap with regions bound by the nucleoid-associated protein Rok, a functional analog of H-NS of Gram-negative bacteria. Rok functions as a negative regulator of at least some horizontally acquired genes. We found that the presence or absence of Rok had little or no effect on insertion site specificity of Tn 916 .},
}

@article {pmid39974991,
year = {2025},
author = {Hullinger, AC and Green, VE and Klancher, CA and Dalia, TN and Dalia, AB},
title = {Two transmembrane transcriptional regulators coordinate to activate chitin-induced natural transformation in Vibrio cholerae.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.09.30.615920},
pmid = {39974991},
issn = {2692-8205},
abstract = {UNLABELLED: Transcriptional regulators are a broad class of proteins that alter gene expression in response to environmental stimuli. Transmembrane transcriptional regulators (TTRs) are a subset of transcriptional regulators in bacteria that can directly regulate gene expression while remaining anchored in the membrane. Whether this constraint impacts the ability of TTRs to bind their DNA targets remains unclear. Vibrio cholerae uses two TTRs, ChiS and TfoS, to activate horizontal gene transfer by natural transformation in response to chitin by inducing the tfoR promoter (P tfoR). While TfoS was previously shown to bind and regulate P tfoR directly, the role of ChiS in P tfoR activation remains unclear. Here, we show that ChiS directly binds P tfoR upstream of TfoS, and that ChiS directly interacts with TfoS. By independently disrupting ChiS-P tfoR and ChiS-TfoS interactions, we show that ChiS-P tfoR interactions play the dominant role in P tfoR activation. Correspondingly, we show that in the absence of ChiS, recruitment of the P tfoR locus to the membrane is sufficient for P tfoR activation when TfoS is expressed at native levels. Finally, we show that the overexpression of TfoS can bypass the need for ChiS for P tfoR activation. All together, these data suggest a model whereby ChiS both (1) recruits the P tfoR DNA locus to the membrane for TfoS and (2) directly interacts with TfoS, thereby recruiting it to the membrane-proximal promoter. This work furthers our understanding of the molecular mechanisms that drive chitin-induced responses in V. cholerae and more broadly highlights how the membrane-embedded localization of TTRs can impact their activity.

AUTHOR SUMMARY: Living organisms inhabit diverse environments where they encounter a wide range of stressors. To survive, they must rapidly sense and respond to their surroundings. One universally conserved mechanism to respond to stimuli is via the action of DNA-binding transcriptional regulators. In bacterial species, these regulators are canonically cytoplasmic proteins that freely diffuse within the cytoplasm. In contrast, an emerging class of transmembrane transcriptional regulators (TTRs) directly regulate gene expression from the cell membrane. Prior work shows that two TTRs, TfoS and ChiS, cooperate to activate horizontal gene transfer by natural transformation in response to chitin in the facultative pathogen Vibrio cholerae . However, how these TTRs coordinate to activate this response has remained unclear. Here, we show that ChiS likely promotes TfoS-dependent activation of natural transformation by (1) relocalizing its target promoter to the membrane and (2) recruiting TfoS to the membrane proximal promoter through a direct interaction. Together, these results inform our understanding of both the V. cholerae chitin response and how TTR function can be impacted by their membrane localization.},
}

@article {pmid39970645,
year = {2025},
author = {Wang, W and Tao, J and Pang, R and Zhang, L and Zhang, Y and Su, Y and Li, W and Hong, S and Kim, H and Zhan, M and Xie, B},
title = {Effect of alkaline-thermal pretreatment on biodegradable plastics degradation and dissemination of antibiotic resistance genes in co-compost system.},
journal = {Journal of hazardous materials},
volume = {489},
number = {},
pages = {137644},
doi = {10.1016/j.jhazmat.2025.137644},
pmid = {39970645},
issn = {1873-3336},
abstract = {Biodegradable plastics (BDPs) are an eco-friendly alternative to traditional plastics in organic waste, but their microbial degradation and impact on antibiotic resistance genes (ARGs) transmission during co-composting remain poorly understood. This study examines how alkaline-thermal pretreatment enhances BDPs degradation and influences the fate of ARGs and mobile genetic elements (MGEs) in co-composting. Pretreatment with 0.1 mol/L NaOH at 100℃ for 40 minutes increased the surface roughness and hydrophilicity of BDPs while reducing their molecular weight and thermal stability. Incorporating pretreated BDPs film (8 g/kg-TS) into the compost reduced the molecular weight of the BDPs by 59.70 % during the maturation stage, facilitating compost heating and prolonging the thermophilic stage. However, incomplete degradation of BDPs releases numerous smaller-sized microplastics, which can act as carriers for microorganisms, facilitating the dissemination of ARGs across environments and posing significant ecological and public health risks. Metagenomic analysis revealed that pretreatment enriched plastic-degrading bacteria, such as Thermobifida fusca, on BDPs surfaces and accelerated microbial plastic degradation during the thermophilic stage, but also increased ARGs abundance. Although pretreatment significantly reduced MGEs abundance (tnpA, IS19), the risk of ARGs dissemination remained. Three plastic-degrading bacteria (Pigmentiphaga sp002188465, Bacillus clausii, and Bacillus altitudinis) were identified as ARGs hosts, underscoring the need to address the risk of horizontal gene transfer of ARGs associated with pretreatment in organic waste management.},
}

@article {pmid39970091,
year = {2024},
author = {Sazykin, IS and Sazykina, MA and Litsevich, AR},
title = {[Distribution of Antibiotic Resistance Genes in Microbial Communities: The Impact of Anthropogenic Pollution].},
journal = {Molekuliarnaia biologiia},
volume = {58},
number = {6},
pages = {937-952},
pmid = {39970091},
issn = {0026-8984},
mesh = {*Bacteria/genetics/drug effects/classification/metabolism ; *Oxidative Stress/drug effects/genetics ; Drug Resistance, Bacterial/genetics/drug effects ; Gene Transfer, Horizontal ; Humans ; Anti-Bacterial Agents/pharmacology ; Environmental Pollution ; Microbiota/drug effects/genetics ; Drug Resistance, Microbial/genetics ; Animals ; Genes, Bacterial ; Wastewater/microbiology ; Evolution, Molecular ; },
abstract = {Issues related to the spread of antibiotic resistance genes in environmental microbial communities are considered. "Hotspots" of adaptive evolution, accumulation, and spread of antibiotic-resistant bacteria and genetic material of antibiotic resistance are highlighted. Such "hotspots" include anthropogenic ecosystems, such as municipal wastewater treatment plants, municipal solid waste landfills, livestock enterprises, and agrocenoses. The influence of various types of pollutants and biotic factors on enhancement of mutagenesis and horizontal transfer of antibiotic resistance genes is considered. The role of mobile genetic elements in mobilization and accelerated spread of resistance determinants is shown. Special attention is paid to the role of oxidative stress and stress regulons, which are activated for realization and control of molecular genetic mechanisms of adaptive evolution of bacteria and the horizontal distribution of genetic material in bacterial populations. Oxidative stress is identified as one of the main activators of genome destabilization and adaptive evolution of bacteria.},
}

*Bacteria/genetics/drug effects/classification/metabolism
*Oxidative Stress/drug effects/genetics
Drug Resistance, Bacterial/genetics/drug effects
Gene Transfer, Horizontal
Humans
Anti-Bacterial Agents/pharmacology
Environmental Pollution
Microbiota/drug effects/genetics
Drug Resistance, Microbial/genetics
Animals
Genes, Bacterial
Wastewater/microbiology
Evolution, Molecular

@article {pmid39869787,
year = {2025},
author = {Lin, C and Li, LJ and Yang, K and Xu, JY and Fan, XT and Chen, QL and Zhu, YG},
title = {Protozoa-enhanced conjugation frequency alters the dissemination of soil antibiotic resistance.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf009},
pmid = {39869787},
issn = {1751-7370},
support = {2021-DST-004//Ningbo S&T project/ ; 2022S117//Ningbo Public Welfare project/ ; 42090063//National Natural Science Foundation of China/ ; },
mesh = {*Conjugation, Genetic ; *Plasmids/genetics ; *Acanthamoeba castellanii/microbiology/genetics ; *Soil Microbiology ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Bacteria/genetics/drug effects ; Metagenomics ; Cercozoa/genetics ; },
abstract = {Protozoa, as primary predators of soil bacteria, represent an overlooked natural driver in the dissemination of antibiotic resistance genes (ARGs). However, the effects of protozoan predation on ARGs dissemination at the community level, along with the underlying mechanisms, remain unclear. Here we used fluorescence-activated cell sorting, qPCR, combined with metagenomics and reverse transcription quantitative PCR, to unveil how protozoa (Colpoda steinii and Acanthamoeba castellanii) influence the plasmid-mediated transfer of ARGs to soil microbial communities. Protozoan predation reduced the absolute abundance of plasmids but promoted the expression of conjugation-associated genes, leading to a 5-fold and 4.5-fold increase in conjugation frequency in the presence of C. steinii and A. castellanii, respectively. Excessive oxidative stress, increased membrane permeability, and the provoked SOS response closely associated with the increased conjugative transfer. Protozoan predation also altered the plasmid host range and selected for specific transconjugant taxa along with ARGs and virulence factors carried by transconjugant communities. This study underscores the role of protozoa in the plasmid-mediated conjugative transfer of ARGs, providing new insights into microbial mechanisms that drive the dissemination of environmental antibiotic resistance.},
}

*Conjugation, Genetic
*Plasmids/genetics
*Acanthamoeba castellanii/microbiology/genetics
*Soil Microbiology
Drug Resistance, Microbial/genetics
Gene Transfer, Horizontal
Bacteria/genetics/drug effects
Metagenomics
Cercozoa/genetics

@article {pmid39970089,
year = {2024},
author = {Shaskolskiy, BL and Kandinov, ID and Gryadunov, DA and Kravtsov, DV},
title = {[Unveiling Neisseria gonorrhoeae Survival: Genetic Variability, Pathogenesis, and Antimicrobial Drug Resistance].},
journal = {Molekuliarnaia biologiia},
volume = {58},
number = {6},
pages = {887-926},
pmid = {39970089},
issn = {0026-8984},
mesh = {*Neisseria gonorrhoeae/genetics/pathogenicity/drug effects/immunology ; Humans ; *Gonorrhea/drug therapy/microbiology/genetics/immunology ; *Drug Resistance, Bacterial/genetics ; Genetic Variation ; Female ; Gene Transfer, Horizontal ; Male ; Anti-Bacterial Agents/therapeutic use/pharmacology ; Immune Evasion/genetics ; Type IV Secretion Systems/genetics ; },
abstract = {Despite nearly a century of therapy for gonococcal infection with a variety of antimicrobials, more than 80 million cases of the disease are reported annually worldwide. The gonorrhea pathogen, Neisseria gonorrhoeae, exhibits an exceptional capability of developing antimicrobial resistance due to its high genetic flexibility. As an obligate pathogen, the gonococcus has evolved mechanisms to evade host defenses by engaging with the innate and adaptive immune responses in both men and women. N. gonorrhoeae can establish residence within epithelial cells, macrophages, and neutrophils. Strains resistant to each of the drugs used in gonorrhea therapy have emerged via genetic variation and horizontal gene transfer. The type IV secretion system plays a critical role in horizontal gene transfer (HGT), driving the evolvement of antimicrobial resistance. The review explores the pathogenesis and immune evasion mechanisms, antimicrobial resistance, genetic variability, laboratory analysis methods for the pathogen, and emerging trends in diagnosis and treatment of gonococcal infections.},
}

*Neisseria gonorrhoeae/genetics/pathogenicity/drug effects/immunology
Humans
*Gonorrhea/drug therapy/microbiology/genetics/immunology
*Drug Resistance, Bacterial/genetics
Genetic Variation
Female
Gene Transfer, Horizontal
Male
Anti-Bacterial Agents/therapeutic use/pharmacology
Immune Evasion/genetics
Type IV Secretion Systems/genetics

@article {pmid39966712,
year = {2025},
author = {Hoile, AE and Holland, PWH and Mulhair, PO},
title = {Gene novelty and gene family expansion in the early evolution of Lepidoptera.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {161},
pmid = {39966712},
issn = {1471-2164},
mesh = {Animals ; *Lepidoptera/genetics ; *Evolution, Molecular ; *Phylogeny ; *Gene Duplication ; *Multigene Family ; Gene Transfer, Horizontal ; Insect Proteins/genetics ; },
abstract = {BACKGROUND: Almost 10% of all known animal species belong to Lepidoptera: moths and butterflies. To understand how this incredible diversity evolved we assess the role of gene gain in driving early lepidopteran evolution. Here, we compared the complete genomes of 115 insect species, including 99 Lepidoptera, to search for novel genes coincident with the emergence of Lepidoptera.

RESULTS: We find 217 orthogroups or gene families which emerged on the branch leading to Lepidoptera; of these 177 likely arose by gene duplication followed by extensive sequence divergence, 2 are candidates for origin by horizontal gene transfer, and 38 have no known homology outside of Lepidoptera and possibly arose via de novo gene genesis. We focus on two new gene families that are conserved across all lepidopteran species and underwent extensive duplication, suggesting important roles in lepidopteran biology. One encodes a family of sugar and ion transporter molecules, potentially involved in the evolution of diverse feeding behaviours in early Lepidoptera. The second encodes a family of unusual propeller-shaped proteins that likely originated by horizontal gene transfer from Spiroplasma bacteria; we name these the Lepidoptera propellin genes.

CONCLUSION: We provide the first insights into the role of genetic novelty in the early evolution of Lepidoptera. This gives new insight into the rate of gene gain during the evolution of the order as well as providing context on the likely mechanisms of origin. We describe examples of new genes which were retained and duplicated further in all lepidopteran species, suggesting their importance in Lepidoptera evolution.},
}

Animals
*Lepidoptera/genetics
*Evolution, Molecular
*Phylogeny
*Gene Duplication
*Multigene Family
Gene Transfer, Horizontal
Insect Proteins/genetics

@article {pmid39966674,
year = {2025},
author = {Mondol, SM and Hossain, MA and Haque, FKM},
title = {Comprehensive genomic insights into a highly pathogenic clone ST656 of mcr8.1 containing multidrug-resistant Klebsiella pneumoniae from Bangladesh.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {5909},
pmid = {39966674},
issn = {2045-2322},
mesh = {*Klebsiella pneumoniae/genetics/drug effects/pathogenicity ; Bangladesh ; *Drug Resistance, Multiple, Bacterial/genetics ; *Genome, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; Humans ; Genomics/methods ; Klebsiella Infections/microbiology ; Virulence Factors/genetics ; Microbial Sensitivity Tests ; Plasmids/genetics ; Colistin/pharmacology ; },
abstract = {Antimicrobial resistance (AMR) is a pressing global health issue, intensified by the spread of resistant pathogens like Klebsiella pneumoniae (K. pneumoniae), which frequently causes hospital-acquired infections. This study focuses on a multidrug-resistant K. pneumoniae sequence type (ST) 656 strain, isolated from canal water in Bangladesh. Whole-genome sequencing and comparative genomic analysis revealed extensive resistance mechanisms and genetic elements underlying its adaptability. The strain exhibited resistance to colistin and multiple β-lactam antibiotics, containing key resistance genes such as mcr8.1, blaLAP-2, blaTEM-1, blaSHV-11 and blaOXA-1, alongside genes for copper, zinc, and silver resistance, indicating survival capability in metal-rich environments. Virulence factor analysis identified genes supporting adhesion, biofilm formation, and immune evasion, amplifying its pathogenic potential. Plasmid and phage analyses revealed mobile genetic elements, highlighting the role of horizontal gene transfer in AMR dissemination. The study included a pangenome analysis using a dataset of 32 publicly available K. pneumoniae sequence type (ST) 656 genomes, demonstrating evidence of an expanding pangenome for K. pneumoniae ST656. This study emphasized the role of environmental sources in AMR spread and the importance of continued surveillance, particularly in settings with intensive antibiotic usage, to mitigate the spread of high-risk, multidrug-resistant clones like K. pneumoniae ST656.},
}

*Klebsiella pneumoniae/genetics/drug effects/pathogenicity
Bangladesh
*Drug Resistance, Multiple, Bacterial/genetics
*Genome, Bacterial
*Anti-Bacterial Agents/pharmacology
Whole Genome Sequencing
Humans
Genomics/methods
Klebsiella Infections/microbiology
Virulence Factors/genetics
Microbial Sensitivity Tests
Plasmids/genetics
Colistin/pharmacology

@article {pmid39965334,
year = {2025},
author = {Zhang, J and Lei, H and Huang, J and Wong, JWC and Li, B},
title = {Co-occurrence and co-expression of antibiotic, biocide, and metal resistance genes with mobile genetic elements in microbial communities subjected to long-term antibiotic pressure: Novel insights from metagenomics and metatranscriptomics.},
journal = {Journal of hazardous materials},
volume = {489},
number = {},
pages = {137559},
doi = {10.1016/j.jhazmat.2025.137559},
pmid = {39965334},
issn = {1873-3336},
abstract = {The burgeoning of antibiotic resistance has emerged as a pressing global challenge. To gain a deeper understanding of the interactions between antibiotic resistance genes (ARGs), biocide and metal resistance genes (BRGs&MRGs), and mobile genetic elements (MGEs), this study utilized metagenomics and metatranscriptomics to investigate their co-occurrence and co-expression in two consortia subjected to long-term exposure to chloramphenicol and lincomycin. Long-term exposure to these antibiotics resulted in significant disparities in resistance profiles: ConsortiumCAP harbored 130 ARGs and 150 BRGs&MRGs, while ConsortiumLIN contained 57 ARGs and 32 BRGs&MRGs. Horizontal gene transfer (HGT) events were predicted at 125 and 300 instances in ConsortiumCAP and ConsortiumLIN, respectively, facilitating the emergence of multidrug-resistant bacteria, such as Caballeronia (10 ARGs, 2 BRGs&MRGs), Cupriavidus (2 ARGs, 10 BRGs&MRGs), and Bacillus (14 ARGs, 21 BRGs&MRGs). Chloramphenicol exposure significantly enriched genes linked to phenicol resistance (floR, capO) and co-expressed ARGs and BRGs&MRGs, while lincomycin exerted narrower effects on resistance genes. Additionally, both antibiotics modulated the expression of degradation genes and virulence factors, highlighting their role in altering bacterial substrate utilization and pathogenic traits. This study provides quantitative insights into the impact of antibiotics on microbial resistance profiles and functions at both DNA and RNA levels, highlighting the importance of reducing antibiotic pollution and limiting the spread of resistance genes in the environment.},
}

@article {pmid39965000,
year = {2025},
author = {Hullinger, AC and Green, VE and Klancher, CA and Dalia, TN and Dalia, AB},
title = {Two transmembrane transcriptional regulators coordinate to activate chitin-induced natural transformation in Vibrio cholerae.},
journal = {PLoS genetics},
volume = {21},
number = {2},
pages = {e1011606},
doi = {10.1371/journal.pgen.1011606},
pmid = {39965000},
issn = {1553-7404},
abstract = {Transcriptional regulators are a broad class of proteins that alter gene expression in response to environmental stimuli. Transmembrane transcriptional regulators (TTRs) are a subset of transcriptional regulators in bacteria that can directly regulate gene expression while remaining anchored in the membrane. Whether this constraint impacts the ability of TTRs to bind their DNA targets remains unclear. Vibrio cholerae uses two TTRs, ChiS and TfoS, to activate horizontal gene transfer by natural transformation in response to chitin by inducing the tfoR promoter (PtfoR). While TfoS was previously shown to bind and regulate PtfoR directly, the role of ChiS in PtfoR activation remains unclear. Here, we show that ChiS directly binds PtfoR upstream of TfoS, and that ChiS directly interacts with TfoS. By independently disrupting ChiS-PtfoR and ChiS-TfoS interactions, we show that ChiS-PtfoR interactions play the dominant role in PtfoR activation. Correspondingly, we show that in the absence of ChiS, recruitment of the PtfoR locus to the membrane is sufficient for PtfoR activation when TfoS is expressed at native levels. Finally, we show that the overexpression of TfoS can bypass the need for ChiS for PtfoR activation. All together, these data suggest a model whereby ChiS both (1) recruits the PtfoR DNA locus to the membrane for TfoS and (2) directly interacts with TfoS, thereby recruiting it to the membrane-proximal promoter. This work furthers our understanding of the molecular mechanisms that drive chitin-induced responses in V. cholerae and more broadly highlights how the membrane-embedded localization of TTRs can impact their activity.},
}

@article {pmid39964597,
year = {2025},
author = {Palanikumar, P and Nathan, B and Muthusamy, K and M, S and Natesan, S and Sampathrajan, V},
title = {Unravelling the Antibiotic Resistance: Molecular Insights and Combating Therapies.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {39964597},
issn = {1559-0291},
abstract = {Antibiotics, the full-stop of invasive bacteria, have been used in clinical setups from unthreatening fever to massive challenging therapies. Constant dependency on medication upsurges the evasion of microbes from antibiotics contemporarily along with ecological footprint. Thus, the infested pathogen became resilient to antibiotics, disguised as multidrug-resistant bacteria (MDR), pandrug-resistant bacteria (PDR), and extensively drug-resistant bacteria (XDR). The etymology of genetic modifications and horizontal gene transfer played an external influence on the arising resurgence. Also, intrinsic parameters, such as antibiotic efflux pumps and the formation of biofilms, encouraged intense resistance to antibiotic drugs. This aggravated resistance in microbes builds up resistome in the environment due to selective pressure; thereby drastic devastation of people suffering from disastrous diseases is mournful. Since novelite approaches for broad-spectrum antibiotics against drug resistance microbes are grueling challenges in these crucial times. This scientific study has come up with neoteric methodologies to elude immediate consequences and health hazards. Inculcating ancestral treatment towards pharmacognosy as adjuvants to the prevailing hi-fi nanotechnology, phage and algal therapy, genome mining, and bioinformatics databases are the optimizing inventions for actual and prospective living.},
}

@article {pmid39960880,
year = {2025},
author = {Zou, W and Ji, Y and Guan, J and Sun, Y},
title = {MOSTPLAS: A Self-correction Multi-label Learning Model for Plasmid Host Range Prediction.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf075},
pmid = {39960880},
issn = {1367-4811},
abstract = {MOTIVATION: Plasmids play an essential role in horizontal gene transfer, aiding their host bacteria in acquiring beneficial traits like antibiotic and metal resistance. There exists some plasmids that can transfer, replicate or persist in multiple organisms. Identifying the relatively complete host range of these plasmids provides insights into how plasmids promote bacterial evolution. To achieve this, we can apply multi-label learning models for plasmid host range prediction. However, there are no databases providing the detailed and complete host labels of these broad-host-range (BHR) plasmids. Without adequate well-annotated training samples, learning models can fail to extract discriminative feature representations for plasmid host prediction.

RESULTS: To address this problem, we propose a self-correction multi-label learning model called MOSTPLAS. We design a pseudo label learning algorithm and a self-correction asymmetric loss to facilitate the training of multi-label learning model with samples containing some unknown missing labels. We conducted a series of experiments on NCBI RefSeq plasmid database, PLSDB 2025 database, plasmids with experimentally determined host labels, Hi-C dataset and DoriC dataset. The benchmark results against other plasmid host range prediction tools demonstrated that MOSTPLAS recognized more host labels while keeping a high precision.

MOSTPLAS is implemented with Python, which can be downloaded at https://github.com/wzou96/MOSTPLAS. All relevant data we used in the experiments can be found at 10.5281/zenodo.14708999.

Please contact: yannisun@cityu.edu.hk. Supplementary data are available at Bioinformatics online.},
}

@article {pmid39960859,
year = {2025},
author = {Chess, MM and Foley, S and Ettensohn, CA},
title = {Horizontal transfer of msp130 genes and the evolution of metazoan biocalcification.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf028},
pmid = {39960859},
issn = {1759-6653},
abstract = {The formation of calcified skeletons is crucial for the development, physiology, and ecology of many marine metazoans. The evolutionary origins of the genetic toolkit required for biocalcification are widely debated. MSP130 proteins, originally identified through their expression specifically by sea urchin skeletal cells, have been hypothesized to have been acquired by metazoans from bacteria through horizontal gene transfer (HGT). Here, we provide support for an HGT-based origin of metazoan MSP130 proteins by conducting phylogenetic and in silico protein analyses utilizing high-quality genomes. We show that msp130 genes underwent duplications within almost all biocalcifying bilaterian phyla and identify highly conserved intron-exon junctions specific to bilaterian msp130 genes. The absence of MSP130 proteins in calcifying, non-bilaterian metazoans and other basal eukaryotes suggests that an ancestral msp130 gene underwent an HGT event that predates bilaterians, but not metazoans. We report striking structural similarities between bilaterian and bacterial MSP130 proteins, with each containing a seven-bladed, barrel-like motif that encompasses a choice-of-anchor domain, and identify highly conserved, predicted Ca2+-binding sites associated with the barrels. These findings point to a conserved, ancient function for MSP130 proteins in biocalcification and support the view that lateral transfer of bacterial genes supported the appearance of calcified animal skeletons.},
}

@article {pmid39955358,
year = {2025},
author = {Mahamud, SMI and Oishy, SH and Roy, S and Pal, K and Rubaiyat, RN and Ansary, MM},
title = {Comparative Genomic Analysis of 66 Bacteriophages Infecting Morganella morganii Strains.},
journal = {Current microbiology},
volume = {82},
number = {4},
pages = {137},
pmid = {39955358},
issn = {1432-0991},
mesh = {*Morganella morganii/virology/genetics ; *Bacteriophages/genetics/classification/isolation & purification ; *Genome, Viral ; *Phylogeny ; *Genomics ; Host Specificity ; Base Composition ; Humans ; },
abstract = {Bacteriophages are viruses that specifically target bacteria and play a crucial role in influencing bacterial evolution and the transmission of antibiotic resistance. In this study, we explored the genomic profiles of 66 bacteriophages that infect Morganella morganii, an opportunistic pathogen associated with difficult-to-treat nosocomial and urinary tract infections. Our findings highlight the extraordinary diversity within this phage population, reflected in their genomic features, evolutionary relationships, and potential contributions to bacterial pathogenicity. The 66 phage genomes exhibited diversity in size, spanning from 6 to 115 kilobase pairs, reflecting a heterogeneous genetic material and coding potential. Their guanine-cytosine (G+C) content varied widely, from 43.3% to 64.6%, suggesting diverse evolutionary origins and adaptive strategies. Phylogenetic analysis identified ten distinct evolutionary clusters, some classified as singletons, highlighting unique evolutionary pathways. Several clusters included phages capable of infecting multiple M. morganii strains, indicating a broader host range and the potential for horizontal gene transfer. Genomic analysis also determined a substantial number of hypothetical proteins, underscoring the need for further investigation to clarify their functions. Importantly, we identified a wide array of antibiotic resistance and virulence-associated genes within these phage genomes, illuminating their potential to impact the treatment of M. morganii infections and develop new, more virulent strains. These findings highlight the critical role of phage-mediated gene transfer in shaping bacterial evolution and facilitating the transmission of antibiotic resistance.},
}

*Morganella morganii/virology/genetics
*Bacteriophages/genetics/classification/isolation & purification
*Genome, Viral
*Phylogeny
*Genomics
Host Specificity
Base Composition
Humans

@article {pmid39954947,
year = {2025},
author = {Saraiva, HCAS and Panzenhagen, P and Santos, AMPD and Portes, AB and Ferreira, JFDS and Junior, CAC},
title = {Unravelling the advances of CRISPR-Cas9 as a precise antimicrobial therapy: a systematic review.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2025.02.002},
pmid = {39954947},
issn = {2213-7173},
abstract = {Antimicrobial resistance (AMR) is a critical public health threat, compromising treatment effectiveness. The spread of resistant pathogens, facilitated by genetic variability and horizontal gene transfer, primarily through plasmids, poses significant challenges to health systems. This review explores the potential of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technology and Cas9 nucleases in combating AMR. The literature review followed the PRISMA guidelines using PubMed, Embase, and Scopus databases until July 2023. The Enterobacterales family, particularly Escherichia coli, was the main focus. The resistance genes targeted were mainly associated with β-lactam antibiotics, specifically bla genes, and colistin resistance linked to the mcr-1 gene. Plasmid vectors have been the primary delivery method for the CRISPR-Cas9 system, with conjugative plasmids resensitizing bacterial strains to various antimicrobials. Other delivery methods included electroporation, phage-mediated delivery, and nanoparticles. The efficacy of the CRISPR-Cas9 system in resensitizing bacterial strains ranged from 4.7% to 100%. Despite challenges in delivery strategies and clinical application, studies integrating nanotechnology present promising approaches to overcome these limitations. This review highlights new perspectives for the clinical use of CRISPR-Cas9 as a specific and efficient antimicrobial agent, potentially replacing traditional broad-spectrum antimicrobials in the future.},
}

@article {pmid39954386,
year = {2025},
author = {Vilar, LC and Rego, ACS and Miguel, MAL and Paranhos, RPDR and Laport, MS and Rossi, CC and Giambiagi-deMarval, M},
title = {Staphylococcus spp. and methicillin-resistance gene mecA dispersion in seawater: A case study of Guanabara Bay's recreational and touristic waters.},
journal = {Comparative immunology, microbiology and infectious diseases},
volume = {118},
number = {},
pages = {102326},
doi = {10.1016/j.cimid.2025.102326},
pmid = {39954386},
issn = {1878-1667},
abstract = {Environmental Staphylococci, particularly coagulase-negative Staphylococci (CoNS), are known reservoirs of antimicrobial resistance genes and human-animal opportunistic pathogens, yet their role within the One Health framework remains underexplored. In this study, we isolated 12 species of CoNS from two sites 10 km apart in Guanabara Bay, Rio de Janeiro, with the most frequent species being the opportunistic Staphylococcus saprophyticus (30.3 %), Staphylococcus warneri (25.7 %), and Staphylococcus epidermidis (16.7 %). GTG5-PCR fingerprinting revealed significant genetic diversity, yet identical profiles persisted across both sites throughout the year, indicating strain dispersion and persistence. Among the 66 strains analyzed, 42 exhibited resistance to clinically significant antimicrobials, including methicillin-resistant strains harboring the mecA gene. Remarkably, 22.7 % of the strains carried CRISPR-Cas systems, a frequency unusually high for Staphylococcus spp., suggesting that bacteriophage pressure in the seawater environment may drive this increase. The presence of antimicrobial-resistant CoNS in Guanabara Bay, a popular recreational area, represents a potential public health risk.},
}

@article {pmid39952999,
year = {2025},
author = {Koper, P and Wysokiński, J and Żebracki, K and Decewicz, P and Dziewit, Ł and Kalita, M and Palusińska-Szysz, M and Mazur, A},
title = {Comparative analysis of Legionella lytica genome identifies specific metabolic traits and virulence factors.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {5554},
pmid = {39952999},
issn = {2045-2322},
support = {2019/03/X/NZ2/00976//Narodowe Centrum Nauki/ ; 2019/03/X/NZ2/00976//Narodowe Centrum Nauki/ ; 2019/03/X/NZ2/00976//Narodowe Centrum Nauki/ ; 2019/03/X/NZ2/00976//Narodowe Centrum Nauki/ ; 2019/03/X/NZ2/00976//Narodowe Centrum Nauki/ ; 2019/03/X/NZ2/00976//Narodowe Centrum Nauki/ ; },
mesh = {*Virulence Factors/genetics ; *Legionella/genetics/pathogenicity ; *Genome, Bacterial ; Plasmids/genetics ; Phylogeny ; Bacterial Proteins/genetics/metabolism ; Virulence/genetics ; Molecular Sequence Annotation ; },
abstract = {The complete genome of Legionella lytica PCM 2298 was sequenced and analyzed to provide insights into its genomic structure, virulence potential, and evolutionary position within the Legionella genus. The genome comprised a 3.2 Mbp chromosome and two plasmids, pLlyPCM2298_1 and pLlyPCM2298_2, contributing to a total genome size of 3.7 Mbp. Functional annotation identified 3,165 coding sequences, including genes associated with known virulence factors such as the major outer membrane protein (MOMP), the macrophage infectivity potentiator (Mip), and a comprehensive set of secretion systems (type II, type IVA, and type IVB Dot/Icm type IV secretion system). Notably, L. lytica contributed 383 unique genes to the Legionella pangenome, with 232 identified effector proteins, of which 35 were plasmid-encoded. The identification of unique genes, particularly those on plasmids, suggests an evolutionary strategy favoring horizontal gene transfer and niche adaptation. The effector repertoire included proteins with domains characteristic of host interaction strategies, such as ankyrin repeats and protein kinases. Comparative analyses showed that while L. lytica shares core virulence traits with other Legionella species, it has distinct features that may contribute to its adaptability and pathogenic potential. These findings underscore the genomic diversity within the genus and contribute to a deeper understanding of Legionella's ecological and clinical significance. A custom web application was developed using the R Shiny library, enabling users to interactively explore the expanded Legionella pangenome through UpSet plots.},
}

*Virulence Factors/genetics
*Legionella/genetics/pathogenicity
*Genome, Bacterial
Plasmids/genetics
Phylogeny
Bacterial Proteins/genetics/metabolism
Virulence/genetics
Molecular Sequence Annotation

@article {pmid39952513,
year = {2025},
author = {Ke, F and Liu, AK and Zhang, QY},
title = {Extra peptidase of a cyanophage confers its stronger lytic effect on bloom-forming Microcystis aeruginosa.},
journal = {International journal of biological macromolecules},
volume = {304},
number = {Pt 2},
pages = {140979},
doi = {10.1016/j.ijbiomac.2025.140979},
pmid = {39952513},
issn = {1879-0003},
abstract = {Microcystis covers important cyanobacteria species that causes harmful algal blooms. Cyanophages are viruses that infect and lyse cyanobacteria and have been considered as potential cyanobacteria control strategy. Present study isolated two cyanophage strains, MaMV-CH01 (CH01) and MaMV-CH02 (CH02), infecting M. aeruginosa. Growth curves showed that CH01 has a stronger proliferation ability and host cell lysis capability than CH02. Combined with genomic, gene structure and function analysis, as well as biologic testing including infectivity, we confirmed that there is widespread horizontal gene transfer between the cyanophages and cyanobacteria, enabling the cyanophages to carry a series of auxiliary metabolic genes (AMG) related to host's metabolism. Moreover, compared with CH02, the cyanophage CH01 carrying extra AMG, a peptidase encoding gene (82R), exhibited stronger lytic activity against its host. Expression of CH01 82R in vitro showed strong bacteriostatic activity. Further, testing the cyanophage's ability to form plaques showed that the CH01(AMG[+]), which encodes the aforementioned peptidase, can form larger plaques, with an area of about threefold than that formed by CH02(AMG[-]). Above results indicated that the cyanophages with specific peptidase possessed stronger algicidal efficiency, which provided a direction for finding efficient cyanophages to regulate the population of bloom-forming cyanobacteria.},
}

@article {pmid39952130,
year = {2025},
author = {Ding, L and Zhang, CM and Jiang, HY},
title = {Lipid-lowering drug clofibric acid promotes conjugative transfer of RP4 plasmid carrying antibiotic resistance genes by multiple mechanisms.},
journal = {Journal of hazardous materials},
volume = {489},
number = {},
pages = {137560},
doi = {10.1016/j.jhazmat.2025.137560},
pmid = {39952130},
issn = {1873-3336},
abstract = {Antibiotic resistance represents a growing global health crisis, predominantly driven by the selective pressure imposed by antibiotics, which facilitates horizontal gene transfer. However, the potential role of non-antibiotic pharmaceuticals in promoting or enabling the spread of antibiotic resistance genes (ARGs) remains poorly understood. This study provided novel insights into the capacity of clofibric acid, a lipid-lowering drug, to enhance the conjugative transfer of ARGs, and deeply explored the underlying multiple mechanisms. The findings revealed that clofibric acid, at concentrations ranging from 0.01 to 1000 μg/L, significantly promoted the transfer efficiency of the RP4 plasmid carrying multiple ARGs. This enhancement was accompanied by a cascade of stress responses in bacterial cells, including elevated production of reactive oxygen species, increased secretion of extracellular polymeric substances, reduced bacterial surface zeta potential, and heightened cell membrane permeability. The physiological alterations were closely linked to significant changes in the expression of genes associated with these processes. Our results highlighted the potential of non-antibiotic pharmaceuticals to contribute to the dissemination of antibiotic resistance, offering a critical foundation for further research into the environmental and public health implications of such compounds.},
}

@article {pmid39913343,
year = {2025},
author = {Davidovich, C and Erokhina, K and Gupta, CL and Zhu, YG and Su, JQ and Djordjevic, SP and Wyrsch, ER and Blum, SE and Cytryn, E},
title = {Occurrence of "under-the-radar" antibiotic resistance in anthropogenically affected produce.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrae261},
pmid = {39913343},
issn = {1751-7370},
mesh = {*Lactuca/microbiology ; *Wastewater/microbiology ; *Escherichia coli/genetics/drug effects/isolation & purification ; *Manure/microbiology ; *Agricultural Irrigation ; Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; Animals ; Plasmids/genetics ; Gene Transfer, Horizontal ; Poultry/microbiology ; Drug Resistance, Bacterial ; },
abstract = {With global climate change, treated-wastewater irrigation and manure amendment are becoming increasingly important in sustainable agriculture in water- and nutrient-stressed regions. Yet, these practices can potentially disseminate pathogens and antimicrobial resistance determinants to crops, resulting in serious health risks to humans through the food chain. Previous studies demonstrated that pathogen and antimicrobial resistance indicators from wastewater and manure survive poorly in the environment, suggesting that ecological barriers prevent their dissemination. However, we recently found that these elements can persist below detection levels in low quality treated wastewater-irrigated soil, and potentially proliferate under favorable conditions. This "under-the-radar" phenomenon was further investigated here, in treated wastewater-irrigated and poultry litter-amended lettuce plants, using an enrichment platform that resembles gut conditions, and an analytical approach that combined molecular and cultivation-based techniques. Enrichment uncovered clinically relevant multidrug-resistant pathogen indicators and a myriad of antibiotic resistance genes in the litter amended and treated wastewater-irrigated lettuce that were not detected by direct analyses, or in the enriched freshwater irrigated samples. Selected resistant E. coli isolates were capable of horizontally transferring plasmids carrying multiple resistance genes to a susceptible strain. Overall, our study underlines the hidden risks of under-the-radar pathogen and antimicrobial resistance determinants in anthropogenically affected agroenvironments, providing a platform to improve quantitative microbial risk assessment models in the future.},
}

*Lactuca/microbiology
*Wastewater/microbiology
*Escherichia coli/genetics/drug effects/isolation & purification
*Manure/microbiology
*Agricultural Irrigation
Anti-Bacterial Agents/pharmacology
Soil Microbiology
Animals
Plasmids/genetics
Gene Transfer, Horizontal
Poultry/microbiology
Drug Resistance, Bacterial

@article {pmid39952116,
year = {2025},
author = {Hirayama, A and Akase, H and Hayase, Y and Maeda, S},
title = {Subminimal inhibitory concentrations of antibiotics and anaerobic conditions promote Escherichia coli cell-to-cell plasmid transformation in biofilms.},
journal = {Biochemical and biophysical research communications},
volume = {752},
number = {},
pages = {151464},
doi = {10.1016/j.bbrc.2025.151464},
pmid = {39952116},
issn = {1090-2104},
abstract = {In recent years, subminimal inhibitory concentrations (sub-MIC) of antibiotics have been found to exert unexpected physiological effects on bacterial cells, beyond their common growth-inhibition properties. Our previous research demonstrated that sub-MIC ampicillin, combined with mild mechanical stimulation using glass balls, significantly promotes intercellular plasmid transformation (cell-to-cell plasmid transformation) in Escherichia coli within air-solid biofilms. In this study, we investigated whether other antibiotics with diverse mechanisms of action similarly enhance plasmid transformation. Our findings revealed that various antibiotics indeed promote cell-to-cell plasmid transformation, and this effect was observed under both aerobic and anaerobic conditions. Interestingly, anaerobic conditions resulted in higher frequencies of plasmid transformation compared to aerobic conditions. Supporting these results, we found that several single-gene knockouts of aerobic respiratory chain components under aerobic conditions also enhanced plasmid transformation. This suggests that the unavailability of aerobic respiration may favor the process of intercellular plasmid transfer. Collectively, our results indicate that a wide range of sub-MIC antibiotics can stimulate horizontal plasmid transfer and that anaerobic conditions are particularly conducive to this process. Based on these findings, we hypothesize that the anaerobic gut environment of antibiotic-treated animals or humans, characterized by biofilm-like high cell densities of antibiotic-exposed bacteria and regular peristaltic and segmental movements, could serve as a favorable niche for horizontal gene transfer via intercellular plasmid transformation.},
}

@article {pmid39950610,
year = {2025},
author = {Jang, YJ and Oh, SD and Hong, JK and Park, JC and Lee, SK and Chang, A and Yun, DW and Lee, B},
title = {Impact of genetically modified herbicide-resistant maize on rhizosphere bacterial communities.},
journal = {GM crops & food},
volume = {16},
number = {1},
pages = {186-198},
doi = {10.1080/21645698.2025.2466915},
pmid = {39950610},
issn = {2164-5701},
mesh = {*Zea mays/genetics/microbiology/growth & development/drug effects ; *Rhizosphere ; *Plants, Genetically Modified/genetics ; *Soil Microbiology ; *Bacteria/genetics/drug effects ; *Herbicides/pharmacology ; *RNA, Ribosomal, 16S/genetics ; Herbicide Resistance/genetics ; Acetyltransferases/genetics ; },
abstract = {Rhizosphere bacterial community studies offer valuable insights into the environmental implications of genetically modified (GM) crops. This study compared the effects of a non-GM maize cultivar, namely Hi-IIA, with those of a herbicide-resistant maize cultivar containing the phosphinothricin N-acetyltransferase gene on the rhizosphere bacterial community across growth stages. 16s rRNA amplicon sequencing and data analysis tools revealed no significant differences in bacterial community composition or diversity between the cultivars. Principal component analysis revealed that differences in community structure were driven by plant growth stages rather than plant type. Polymerase chain reaction analysis was conducted to examine the potential horizontal transfer of the introduced gene from the GM maize to rhizosphere microorganisms; however, the introduced gene was not detected in the soil genomic DNA. Overall, the environmental impact of GM maize, particularly on soil microorganisms, is negligible, and the cultivation of GM maize does not alter significantly the rhizosphere bacterial community.},
}

*Zea mays/genetics/microbiology/growth & development/drug effects
*Rhizosphere
*Plants, Genetically Modified/genetics
*Soil Microbiology
*Bacteria/genetics/drug effects
*Herbicides/pharmacology
*RNA, Ribosomal, 16S/genetics
Herbicide Resistance/genetics
Acetyltransferases/genetics

@article {pmid39947201,
year = {2025},
author = {Yang, SNN and Kertesz, MA and Coleman, NV},
title = {Phylogenetic and Functional Diversity of Soluble Di-Iron Monooxygenases.},
journal = {Environmental microbiology},
volume = {27},
number = {2},
pages = {e70050},
pmid = {39947201},
issn = {1462-2920},
support = {//University of Sydney/ ; },
mesh = {*Phylogeny ; *Mixed Function Oxygenases/genetics/metabolism/chemistry ; *Bacteria/enzymology/genetics/classification ; Biodegradation, Environmental ; Gene Transfer, Horizontal ; Substrate Specificity ; Oxidation-Reduction ; Oxygenases/genetics/metabolism ; Bacterial Proteins/genetics/metabolism/chemistry ; Iron/metabolism ; },
abstract = {Monooxygenase (MO) enzymes are responsible for the oxidation of hydrocarbons and other compounds in the carbon and nitrogen cycles, are important for the biodegradation of pollutants and can act as biocatalysts for chemical manufacture. The soluble di-iron monooxygenases (SDIMOs) are of interest due to their broad substrate range, high enantioselectivity and ability to oxidise inert substrates such as methane. Here, we re-examine the phylogeny and functions of these enzymes, using recent advances in the field and expansions in sequence diversity in databases to highlight relationships between SDIMOs and revisit their classification. We discuss the impact of horizontal gene transfer on SDIMO phylogeny, the potential of SDIMOs for the biodegradation of pollutants and the importance of heterologous expression as a tool for understanding SDIMO functions and enabling their use as biocatalysts. Our analysis highlights current knowledge gaps, most notably, the unknown substrate ranges and physiological roles of enzymes that have so far only been detected via genome or metagenome sequencing. Enhanced understanding of the diversity and functions of the SDIMO enzymes will enable better prediction and management of biogeochemical processes and also enable new applications of these enzymes for biocatalysis and bioremediation.},
}

*Phylogeny
*Mixed Function Oxygenases/genetics/metabolism/chemistry
*Bacteria/enzymology/genetics/classification
Biodegradation, Environmental
Gene Transfer, Horizontal
Substrate Specificity
Oxidation-Reduction
Oxygenases/genetics/metabolism
Bacterial Proteins/genetics/metabolism/chemistry
Iron/metabolism

@article {pmid39947132,
year = {2025},
author = {Wittmers, F and Poirier, C and Bachy, C and Eckmann, C and Matantseva, O and Carlson, CA and Giovannoni, SJ and Goodenough, U and Worden, AZ},
title = {Symbionts of predatory protists are widespread in the oceans and related to animal pathogens.},
journal = {Cell host & microbe},
volume = {33},
number = {2},
pages = {182-199.e7},
doi = {10.1016/j.chom.2025.01.009},
pmid = {39947132},
issn = {1934-6069},
mesh = {*Symbiosis ; Animals ; *Choanoflagellata/physiology ; *Oceans and Seas ; *Phylogeny ; Humans ; Bacteria/genetics/classification ; Gene Transfer, Horizontal ; Genome, Bacterial ; Fishes/microbiology ; Eukaryota/physiology/genetics ; Microbiota ; },
abstract = {Protists are major predators of ocean microbial life, with an ancient history of entanglements with prokaryotes, but their delicate cell structures and recalcitrance to culturing hinder exploration of marine symbioses. We report that tiny oceanic protistan predators, specifically choanoflagellates-the closest living unicellular relatives of animals-and uncultivated MAST-3 form symbioses with four bacterial lineages related to animal symbionts. By targeting living phagotrophs on ship expeditions, we recovered genomes from physically associated uncultivated Legionellales and Rickettsiales. The evolutionary trajectories of Marinicoxiellaceae, Cosmosymbacterales, Simplirickettsiaceae, and previously named Gamibacteraceae vary, including host-engagement mechanisms unknown in marine bacteria, horizontally transferred genes that mediate pathogen-microbiome interactions, and nutritional pathways. These symbionts and hosts occur throughout subtropical and tropical oceans. Related bacteria were detected in public data from freshwater, fish, and human samples. Symbiont associations with animal-related protists, alongside relationships to animal pathogens, suggest an unexpectedly long history of shifting associations and possibilities for host expansion as environments change.},
}

*Symbiosis
Animals
*Choanoflagellata/physiology
*Oceans and Seas
*Phylogeny
Humans
Bacteria/genetics/classification
Gene Transfer, Horizontal
Genome, Bacterial
Fishes/microbiology
Eukaryota/physiology/genetics
Microbiota

@article {pmid39946809,
year = {2025},
author = {Zeng, Q and Pu, Y and Liu, Q and Li, Y and Sun, Y and Hao, Y and Yang, Q and Yang, B and Wu, Y and Shi, S and Gong, Z},
title = {Effects of decabromodiphenyl ethane (DBDPE) exposure on soil microbial community: Nitrogen cycle, microbial defense and repair and antibiotic resistance genes transfer.},
journal = {Journal of environmental management},
volume = {376},
number = {},
pages = {124503},
doi = {10.1016/j.jenvman.2025.124503},
pmid = {39946809},
issn = {1095-8630},
abstract = {DBDPE, a widely used brominated flame retardant, is frequently detected in soil. However, the toxic effects of DBDPE on soil microbial communities remain unclear. This study investigated the effects of DBDPE on the microbial community shifts, the nitrogen cycle, microbial defense and repair, and antibiotic resistance genes (ARGs) transfer. After 28 days of DBDPE exposure, the soil microbial community was altered. Denitrifier were enriched by 4.07-78.22% under DBDPE exposure concentrations of 100-1000 ng/g. Additionally, the abundances of genes encoding enzymes involved in nitrification and denitrification processes were up-regulated at 100 ng/g DBDPE exposure, and further promoted at 1000 ng/g DBDPE exposure. Meanwhile, DBDPE exposure at concentrations of 100-1000 ng/g stimulated the production of extracellular polymers substances (EPS) (2155-2347 mg/kg), increased the accumulation of reactive oxygen species (ROS) (by 97.95-108.38%), and activated the antioxidant defense system of soil microorganisms, which correspondingly down-regulated catalase (CAT) genes (by 4.65-4.91%), while up-regulated superoxide dismutase (SOD) (by 0.52-2.63%) and glutathione (GSH) genes (by 19.03%-44.61%). Genes related to the tricarboxylic acid (TCA) cycle, glycerophospholipid metabolism, and peptidoglycan biosynthesis were up-regulated, enhancing cell membrane repair in response to DBDPE exposure. Moreover, the increase in DBDPE concentration selectively enriched and promoted the transmission of ARGs. The co-occurrence network of ARGs and mobile genetic elements (MGEs) revealed that DBDPE facilitated the horizontal gene transfer (HGT)-mediated transmission of transposase, ist, and insertion sequence-associated ARGs.},
}

@article {pmid39946805,
year = {2025},
author = {Xu, Z and Li, C and Xiong, J and Hu, S and Ma, Y and Li, S and Ren, X and Huang, B and Pan, X},
title = {The ecological security risks of phthalates: A focus on antibiotic resistance gene dissemination in aquatic environments.},
journal = {Journal of environmental management},
volume = {376},
number = {},
pages = {124488},
doi = {10.1016/j.jenvman.2025.124488},
pmid = {39946805},
issn = {1095-8630},
abstract = {Antibiotic resistance genes (ARGs) have become a major focus in environmental safety and human health, with concerns about non-antibiotic substances like microplastics facilitating their horizontal gene transfer. Phthalate esters (PAEs), as ubiquitous plastic additives, are prevalent in aquatic environments, yet there remains a dearth of studies examining their impacts on ARG dissemination. This study focuses on dibutyl phthalate (DBP), a prototypical PAE, to assess its potential influence on the conjugative transfer of ARGs along with the related molecular mechanisms. The results revealed that DBP exposure at environmentally relevant concentrations significantly promoted the conjugative transfer of RP4 plasmid-mediated ARGs by up to 2.7-fold compared to that of the control group, whereas it severely suppressed the conjugation at a high concentration (100 μg/L). The promotion of conjugation transfer by low-concentration DBP (0.01-10 μg/L) was mainly attributed to the stimulation of ROS, enhanced membrane permeability, increased energy synthesis, increased polymeric substances secretion, and upregulation of conjugation-related genes. Conversely, high DBP exposure induced oxidative damage and reduced ATP synthesis, resulting in the suppression of ARG conjugation. Notably, donor and recipient bacteria responded differently to DBP-induced oxidative stress. This study explores the environmental behavior of DBP in the water environment from the perspective of ARG propagation and provides essential data and theoretical insights to raise public awareness about the ecological security risks of PAEs.},
}

@article {pmid39945525,
year = {2025},
author = {Chang, TH and Pourtois, JD and Haddock, NL and Furukawa, D and Kelly, KE and Amanatullah, DF and Burgener, E and Milla, C and Banaei, N and Bollyky, PL},
title = {Prophages are infrequently associated with antibiotic resistance in Pseudomonas aeruginosa clinical isolates.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0090424},
doi = {10.1128/msphere.00904-24},
pmid = {39945525},
issn = {2379-5042},
abstract = {Lysogenic bacteriophages can integrate their genome into the bacterial chromosome in the form of a prophage and can promote genetic transfer between bacterial strains in vitro. However, the contribution of lysogenic bacteriophages to the incidence of antimicrobial resistance (AMR) in clinical settings is poorly understood. Here, in a set of 186 clinical isolates of Pseudomonas aeruginosa collected from respiratory cultures from 82 patients with cystic fibrosis, we evaluate the links between prophage counts and both genomic and phenotypic resistance to six anti-pseudomonal antibiotics: tobramycin, colistin, ciprofloxacin, meropenem, aztreonam, and piperacillin-tazobactam. We identified 239 different prophages in total. We find that P. aeruginosa isolates contain on average 3.06 ± 1.84 (SD) predicted prophages. We find no significant association between the number of prophages per isolate and the minimum inhibitory concentration for any of these antibiotics. We then investigate the relationship between particular prophages and AMR. We identify a single lysogenic phage associated with phenotypic resistance to the antibiotic tobramycin and, consistent with this association, we observe that AMR genes associated with resistance to tobramycin are more likely to be found when this prophage is present. However, we find that they are not encoded directly on prophage sequences. Additionally, we identify a single prophage statistically associated with ciprofloxacin resistance but do not identify any genes associated with ciprofloxacin phenotypic resistance. These findings suggest that prophages are only infrequently associated with the AMR genes in clinical isolates of P. aeruginosa.IMPORTANCEAntibiotic-resistant infections of Pseudomonas aeruginosa (Pa), a leading pathogen in patients with cystic fibrosis (CF), are a global health threat. While lysogenic bacteriophages are known to facilitate horizontal gene transfer, their role in promoting antibiotic resistance in clinical settings remains poorly understood. In our analysis of 186 clinical isolates of P. aeruginosa from CF patients, we find that prophage abundance does not predict phenotypic resistance to key antibiotics but that specific prophages are infrequently associated with tobramycin resistance genes. In addition, we do not find antimicrobial resistance (AMR) genes encoded directly on prophages. These results highlight that while phages can be associated with AMR, phage-mediated AMR transfer may be rare in clinical isolates and difficult to identify. This work is important for future efforts on mitigating AMR in CFCF and other vulnerable populations affected by Pa infections and advances our understanding of bacterial-phage dynamics in clinical infections.},
}

@article {pmid39940717,
year = {2025},
author = {Subramanian, P and Kim, D and Ko, HR and Sim, JS and Mani, V and Lee, CM and Lee, SK and Park, S and Kim, DG and Yu, Y and Hahn, BS},
title = {Genomic and Transcriptomic Analysis of the Polyploidy Cyst Nematode, Heterodera trifolii, and Heterodera schachtii.},
journal = {International journal of molecular sciences},
volume = {26},
number = {3},
pages = {},
pmid = {39940717},
issn = {1422-0067},
support = {PJ01333201//Rural Development Administration/ ; },
mesh = {Animals ; *Polyploidy ; *Tylenchoidea/genetics ; Transcriptome/genetics ; Genome, Helminth ; Gene Expression Profiling/methods ; Genomics/methods ; Phylogeny ; Female ; Gene Transfer, Horizontal ; },
abstract = {Cyst nematodes remain a major threat to global agricultural production, causing huge losses. To understand the parasitism of the cyst nematodes Heterodera trifolii (HT) and Heterodera schachtii (HS), we constructed whole-genome assemblies using short- and long-read sequencing technologies. The nematode genomes were 379 Mb and 183 Mb in size, with the integrated gene models predicting 40,186 and 18,227 genes in HT and HS, respectively. We found more than half of the genes predicted in HT (64.7%) and HS (53.2%) were collinear to their nearest neighbor H. glycines (HG). Large-scale duplication patterns in HT and segmental duplications of more than half of the orthologous genes indicate that the genome of HT is polyploid in nature. Functional analysis of the genes indicated that 65.6% of the HG genes existed within the HT genome. Most abundant genes in HT and HS were involved in gene regulation, DNA integration, and chemotaxis. Differentially expressed genes showed upregulation of cuticle structural constituent genes during egg and female stages and cytoskeletal motor activity-related genes in juvenile stage 2 (J2). Horizontal gene transfer analyses identified four new vitamin biosynthesis genes, pdxK, pdxH, pdxS, and fabG, of bacterial origin, to be first reported in HT and HS. Mitogenomes of HT, HS, and HG showed similar structure, composition, and codon usage. However, rates of substitution of bases in the gene nad4l were significantly different between HT and HS. The described genomes, transcriptomes, and mitogenomes of plant-parasitic nematodes HT and HS are potential bio-resources used to identify several strategies of control of the nematode.},
}

Animals
*Polyploidy
*Tylenchoidea/genetics
Transcriptome/genetics
Genome, Helminth
Gene Expression Profiling/methods
Genomics/methods
Phylogeny
Female
Gene Transfer, Horizontal

@article {pmid39939755,
year = {2025},
author = {Subramanian, S and Kerns, HR and Braverman, SG and Doore, SM},
title = {The structure of Shigella virus Sf14 reveals the presence of two decoration proteins and two long tail fibers.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {222},
pmid = {39939755},
issn = {2399-3642},
support = {R01 AI170608/AI/NIAID NIH HHS/United States ; U24 GM116789/GM/NIGMS NIH HHS/United States ; AI170608//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; U24GM116789-03//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
mesh = {*Capsid Proteins/chemistry/metabolism/genetics ; *Bacteriophages/genetics/metabolism/chemistry ; Shigella flexneri/virology/genetics/metabolism ; Models, Molecular ; Phylogeny ; Capsid/metabolism/chemistry ; Protein Conformation ; },
abstract = {Bacteriophage Sf14 infects the human pathogen Shigella flexneri. A previous low-resolution structure suggested the presence of a decoration protein on its T = 9 icosahedral capsid. Here, we determined high-resolution structures of the Sf14 capsid and neck, along with a moderate-resolution structure of the whole Sf14 tail and baseplate. These structures indicate the capsid has not one, but two different types of decoration proteins: a trimeric β-tulip lattice that covers the entire capsid and a set of Hoc-like proteins that bind preferentially to hexamers at the quasi-3-fold axes of symmetry. The neck also contains two sets of whiskers oriented in opposite directions, and the tail has two types of long tail fibers which may bind different receptors. Based on homology and phylogenetic analysis, Sf14 may be the product of multiple horizontal gene transfer events. The structures presented here can be used to investigate further hypotheses of phage structure-function relationships and structural diversity.},
}

*Capsid Proteins/chemistry/metabolism/genetics
*Bacteriophages/genetics/metabolism/chemistry
Shigella flexneri/virology/genetics/metabolism
Models, Molecular
Phylogeny
Capsid/metabolism/chemistry
Protein Conformation

@article {pmid39892320,
year = {2025},
author = {Huang, L and Dai, W and Sun, X and Pu, Y and Feng, J and Jin, L and Sun, K},
title = {Diet-driven diversity of antibiotic resistance genes in wild bats: implications for public health.},
journal = {Microbiological research},
volume = {293},
number = {},
pages = {128086},
doi = {10.1016/j.micres.2025.128086},
pmid = {39892320},
issn = {1618-0623},
mesh = {Animals ; *Chiroptera/microbiology ; *Diet/veterinary ; *Gastrointestinal Microbiome/drug effects/genetics ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Anti-Bacterial Agents/pharmacology ; Public Health ; Drug Resistance, Bacterial/genetics ; Metagenomics ; Genes, Bacterial ; Interspersed Repetitive Sequences ; Animals, Wild/microbiology ; Gene Transfer, Horizontal ; Humans ; Drug Resistance, Microbial/genetics ; },
abstract = {Wild bats may serve as reservoirs for antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria, potentially contributing to antibiotic resistance and pathogen transmission. However, current assessments of bats' antibiotic resistance potential are limited to culture-dependent bacterial snapshots. In this study, we present metagenomic evidence supporting a strong association between diet, gut microbiota, and the resistome, highlighting bats as significant vectors for ARG propagation. We characterized gut microbiota, ARGs, and mobile genetic elements (MGEs) in bats with five distinct diets: frugivory, insectivory, piscivory, carnivory, and sanguivory. Our analysis revealed high levels of ARGs in bat guts, with limited potential for horizontal transfer, encompassing 1106 ARGs conferring resistance to 26 antibiotics. Multidrug-resistant and polymyxin-resistant genes were particularly prevalent among identified ARG types. The abundance and diversity of ARGs/MGEs varied significantly among bats with different dietary habits, possibly due to diet-related differences in microbial composition. Additionally, genetic linkage between high-risk ARGs and multiple MGEs was observed on the genomes of various zoonotic pathogens, indicating a potential threat to human health from wild bats. Overall, our study provides a comprehensive analysis of the resistome in wild bats and underscores the role of dietary habits in wildlife-associated public health risks.},
}

Animals
*Chiroptera/microbiology
*Diet/veterinary
*Gastrointestinal Microbiome/drug effects/genetics
*Bacteria/genetics/classification/drug effects/isolation & purification
*Anti-Bacterial Agents/pharmacology
Public Health
Drug Resistance, Bacterial/genetics
Metagenomics
Genes, Bacterial
Interspersed Repetitive Sequences
Animals, Wild/microbiology
Gene Transfer, Horizontal
Humans
Drug Resistance, Microbial/genetics

@article {pmid39939538,
year = {2025},
author = {Li, ZZ and Wang, Y and He, XY and Li, WG},
title = {The Taihangia mitogenome provides new insights into its adaptation and organelle genome evolution in Rosaceae.},
journal = {Planta},
volume = {261},
number = {3},
pages = {59},
pmid = {39939538},
issn = {1432-2048},
support = {31370434//National Natural Science Foundation of China/ ; },
mesh = {*Genome, Mitochondrial/genetics ; *Phylogeny ; *Rosaceae/genetics ; *Evolution, Molecular ; Genome, Plant/genetics ; Adaptation, Physiological/genetics ; Plastids/genetics ; Gene Transfer, Horizontal ; },
abstract = {We present the first Taihangia mitogenome, uncovering frequent rearrangements and significant length variation in Rosaceae, likely driven by hybridization and repeat content, alongside widespread mito-chloroplast phylogenetic conflicts. Taihangia, an ancient and endangered monotypic genus within the subfamily Rosoideae of the family Rosaceae, is endemic to cliffs and serves as an ideal material for studying the adaptations of cliff-dwelling plants and the evolutionary processes of the Rosaceae family. In this study, the mitogenome and plastome of T. rupestris var. ciliata were assembled, with lengths of 265,633 bp and 155,467 bp, both exhibiting typical circular structures. Positive selection was detected in the nad4L and sdh4 genes, likely playing a role in adaptation to harsh environments. Comparative genomic analysis indicated that repetitive sequences are likely the main contributors to genome size variation in Rosaceae and also influence horizontal gene transfer between organelle genomes. In T. rupestris var. ciliata, 20 mitochondrial plastid DNA sequences were identified, including 16 complete plastid genes. Moreover, frequent rearrangements were observed in the non-coding regions of mitogenome within the subfamily Rosoideae, potentially linked to the complex evolutionary history and the presence of repetitive sequences. In contrast, coding regions remained highly conserved (over 83% similarity) to maintain essential mitochondrial functions. Phylogenomic analysis of the two organelle genomes revealed conflicts in the phylogenetic relationships within Rosaceae, potentially due to the inconsistent mutation rates and frequent hybridization events in the evolutionary history of the family. In conclusion, the organelle genome analysis of Taihangia provides crucial genomic resources for understanding the evolution and adaptation of Rosaceae species.},
}

*Genome, Mitochondrial/genetics
*Phylogeny
*Rosaceae/genetics
*Evolution, Molecular
Genome, Plant/genetics
Adaptation, Physiological/genetics
Plastids/genetics
Gene Transfer, Horizontal

@article {pmid39919124,
year = {2025},
author = {Rodriguez-Grande, J and Ortiz, Y and Garcia-Lopez, D and Garcillán-Barcia, MP and de la Cruz, F and Fernandez-Lopez, R},
title = {Encounter rates and engagement times limit the transmission of conjugative plasmids.},
journal = {PLoS genetics},
volume = {21},
number = {2},
pages = {e1011560},
doi = {10.1371/journal.pgen.1011560},
pmid = {39919124},
issn = {1553-7404},
mesh = {*Plasmids/genetics ; *Conjugation, Genetic ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Escherichia coli/genetics ; Bacteria/genetics ; },
abstract = {Plasmid conjugation is a major route for the dissemination of antibiotic resistances and adaptive genes among bacterial populations. Obtaining precise conjugation rates is thus key to understanding how antibiotic resistances spread. Plasmid conjugation is typically modeled as a density-dependent process, where the formation of new transconjugants depends on the rate of encounters between donor and receptor cells. By analyzing conjugation dynamics at different cell concentrations, here we show that this assumption only holds at very low bacterial densities. At higher cell concentrations, conjugation becomes limited by the engagement time, the interval required between two successful matings. Plasmid conjugation therefore follows a Holling´s Type II functional response, characterized by the encounter rate and the engagement time, which represent, respectively, the density and frequency-dependent limits of plasmid transmission. Our results demonstrate that these parameters are characteristic of the transfer machinery, rather than the entire plasmid genome, and that they are robust to environmental and transcriptional perturbation. Precise parameterization of plasmid conjugation will contribute to better understanding the propagation dynamics of antimicrobial resistances.},
}

*Plasmids/genetics
*Conjugation, Genetic
Drug Resistance, Bacterial/genetics
Gene Transfer, Horizontal
Escherichia coli/genetics
Bacteria/genetics

@article {pmid39937386,
year = {2025},
author = {Lindeberg, A and Hellmuth, M},
title = {Simplifying and Characterizing DAGs and Phylogenetic Networks via Least Common Ancestor Constraints.},
journal = {Bulletin of mathematical biology},
volume = {87},
number = {3},
pages = {44},
pmid = {39937386},
issn = {1522-9602},
mesh = {*Phylogeny ; *Mathematical Concepts ; *Models, Genetic ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Algorithms ; Animals ; },
abstract = {Rooted phylogenetic networks, or more generally, directed acyclic graphs (DAGs), are widely used to model species or gene relationships that traditional rooted trees cannot fully capture, especially in the presence of reticulate processes or horizontal gene transfers. Such networks or DAGs are typically inferred from observable data (e.g., genomic sequences of extant species), providing only an estimate of the true evolutionary history. However, these inferred DAGs are often complex and difficult to interpret. In particular, many contain vertices that do not serve as least common ancestors (LCAs) for any subset of the underlying genes or species, thus may lack direct support from the observable data. In contrast, LCA vertices are witnessed by historical traces justifying their existence and thus represent ancestral states substantiated by the data. To reduce unnecessary complexity and eliminate unsupported vertices, we aim to simplify a DAG to retain only LCA vertices while preserving essential evolutionary information. In this paper, we characterize LCA -relevant and lca -relevant DAGs, defined as those in which every vertex serves as an LCA (or unique LCA) for some subset of taxa. We introduce methods to identify LCAs in DAGs and efficiently transform any DAG into an LCA -relevant or lca -relevant one while preserving key structural properties of the original DAG or network. This transformation is achieved using a simple operator " ⊖ " that mimics vertex suppression.},
}

*Phylogeny
*Mathematical Concepts
*Models, Genetic
*Evolution, Molecular
Gene Transfer, Horizontal
Algorithms
Animals

@article {pmid39936903,
year = {2025},
author = {Elena, AX and Orel, N and Fang, P and Herndl, GJ and Berendonk, TU and Tinta, T and Klümper, U},
title = {Jellyfish blooms-an overlooked hotspot and potential vector for the transmission of antimicrobial resistance in marine environments.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0101224},
doi = {10.1128/msystems.01012-24},
pmid = {39936903},
issn = {2379-5077},
abstract = {Gelatinous zooplankton (GZ) represents an important component of marine food webs, capable of generating massive blooms with severe environmental impact. When these blooms collapse, considerable amounts of organic matter (GZ-OM) either sink to the seafloor or can be introduced into the ocean's interior, promoting bacterial growth and providing a colonizable surface for microbial interactions. We hypothesized that GZ-OM is an overlooked marine hotspot for transmitting antimicrobial resistance genes (ARGs). To test this, we first re-analyzed metagenomes from two previous studies that experimentally evolved marine microbial communities in the presence and absence of OM from Aurelia aurita and Mnemiopsis leidyi recovered from bloom events and thereafter performed additional time-resolved GZ-OM degradation experiments to improve sample size and statistical power of our analysis. We analyzed these communities for composition, ARG, and mobile genetic element (MGE) content. Communities exposed to GZ-OM displayed up to fourfold increased relative ARG and up to 10-fold increased MGE abundance per 16S rRNA gene copy compared to the controls. This pattern was consistent across ARG and MGE classes and independent of the GZ species, indicating that nutrient influx and colonizable surfaces drive these changes. Potential ARG carriers included genera containing potential pathogens raising concerns of ARG transfer to pathogenic strains. Vibrio was pinpointed as a key player associated with elevated ARGs and MGEs. Whole-genome sequencing of a Vibrio isolate revealed the genetic capability for ARG mobilization and transfer. This study establishes the first link between two emerging issues of marine coastal zones, jellyfish blooms and ARG spread, both likely increasing with future ocean change. Hence, jellyfish blooms are a quintessential "One Health" issue where decreasing environmental health directly impacts human health.IMPORTANCEJellyfish blooms are, in the context of human health, often seen as mainly problematic for oceanic bathing. Here we demonstrate that they may also play a critical role as marine environmental hotspots for the transmission of antimicrobial resistance (AMR). This study employed (re-)analyses of microcosm experiments to investigate how particulate organic matter introduced to the ocean from collapsed jellyfish blooms, specifically Aurelia aurita and Mnemiopsis leidyi, can significantly increase the presence of antimicrobial resistance genes and mobile genetic elements in marine microbial communities by up to one order of magnitude. By providing abundant nutrients and surfaces for bacterial colonization, organic matter from these blooms enhances ARG proliferation, including transfer to and mobility in potentially pathogenic bacteria like Vibrio. Understanding this connection highlights the importance of monitoring jellyfish blooms as part of marine health assessments and developing strategies to mitigate the spread of AMR in coastal ecosystems.},
}

@article {pmid39935761,
year = {2025},
author = {Wijaya, AJ and Anžel, A and Richard, H and Hattab, G},
title = {Current state and future prospects of Horizontal Gene Transfer detection.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {1},
pages = {lqaf005},
pmid = {39935761},
issn = {2631-9268},
mesh = {*Gene Transfer, Horizontal ; *Artificial Intelligence ; Computational Biology/methods ; },
abstract = {Artificial intelligence (AI) has been shown to be beneficial in a wide range of bioinformatics applications. Horizontal Gene Transfer (HGT) is a driving force of evolutionary changes in prokaryotes. It is widely recognized that it contributes to the emergence of antimicrobial resistance (AMR), which poses a particularly serious threat to public health. Many computational approaches have been developed to study and detect HGT. However, the application of AI in this field has not been investigated. In this work, we conducted a review to provide information on the current trend of existing computational approaches for detecting HGT and to decipher the use of AI in this field. Here, we show a growing interest in HGT detection, characterized by a surge in the number of computational approaches, including AI-based approaches, in recent years. We organize existing computational approaches into a hierarchical structure of computational groups based on their computational methods and show how each computational group evolved. We make recommendations and discuss the challenges of HGT detection in general and the adoption of AI in particular. Moreover, we provide future directions for the field of HGT detection.},
}

*Gene Transfer, Horizontal
*Artificial Intelligence
Computational Biology/methods

@article {pmid39933461,
year = {2025},
author = {Mortezaei, Y and Gaballah, MS and Demirer, GN and Lammers, RW and Williams, MR},
title = {From wastewater to sludge: The role of microplastics in shaping anaerobic digestion performance and antibiotic resistance gene dynamics.},
journal = {Journal of hazardous materials},
volume = {489},
number = {},
pages = {137413},
doi = {10.1016/j.jhazmat.2025.137413},
pmid = {39933461},
issn = {1873-3336},
abstract = {The presence of microplastics (MPs) in wastewater treatment plants (WWTPs) disrupt processes and threaten the effectiveness of anaerobic digestion (AD), raising critical environmental and operational concerns. This review assesses MP occurrence in WWTPs and its effects on biogas production and the fate of antibiotic resistance genes (ARGs) during AD to understand their impact on process efficiency and environmental health. Polypropylene (PP) and polyethylene (PE) are the most prevalent types of MPs which are found in WWTP influent at an average concentration of 801.5 particles per liter (P/L), decrease to 38.3 P/L in effluent, and accumulate in sludge at 70.5 P/L. The effect of MPs on AD performance is influenced by MP type, concentration, size, and AD conditions (i.e., feed substrate, reactor configuration, temperature, and incubation time). For example, certain MPs (polyamide 7 (PA7) and PP) increase methane production by 39.5 %, while aged MPs decrease it by 47.2 %. The review also explores how AD drives MP degradation mechanisms like oxidation, hydrolysis, mechanical stress, and biodegradation. Additionally, MPs significantly impact ARGs, with abundance increasing by 0.4-514.4 %, especially with aged MPs. Mechanistic effects of MPs on ARGs dissemination were also discussed, including horizontal gene transfer (reactive oxygen species production, cell membrane permeability, extracellular polymeric substances secretion, and ATP dynamics), vertical gene transfer, microbial community, and adsorbing pollutants. This analysis provides insights into the complex interactions between MPs, microbial processes, and ARGs, highlighting their implications for wastewater treatment and biogas production systems.},
}

@article {pmid39931631,
year = {2024},
author = {Zhou, X and Wagh, K and Lv, G and Sharma, D and Lei, W},
title = {Genome drafting of nosocomial infection CRE Klebsiella pneumoniae confirming resistance to colistin and eravacycline, carrying bla NDM-1, mcr-1, and bla KPC-2, in neonatology from November to December 2023.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1528017},
pmid = {39931631},
issn = {2235-2988},
mesh = {Humans ; *Klebsiella pneumoniae/genetics/drug effects/isolation & purification ; *Klebsiella Infections/microbiology/epidemiology ; *Cross Infection/microbiology ; Infant, Newborn ; *Colistin/pharmacology ; *beta-Lactamases/genetics ; *Anti-Bacterial Agents/pharmacology ; *Whole Genome Sequencing ; *Intensive Care Units, Neonatal ; *Disease Outbreaks ; *Genome, Bacterial/genetics ; *Microbial Sensitivity Tests ; Drug Resistance, Multiple, Bacterial/genetics ; Plasmids/genetics ; Neonatology ; Bacterial Proteins/genetics ; Carbapenem-Resistant Enterobacteriaceae/genetics/isolation & purification/drug effects ; Male ; },
abstract = {BACKGROUND: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a critical pathogen in healthcare settings, associated with high mortality due to its extensive antibiotic resistance. In this study, we report an outbreak of CRKP in a neonatal intensive care unit (NICU) within a 200-bed tertiary hospital. The main goal of this study was to characterize the phenotypic and genomic profiles of the CRKP isolates involved in the outbreak and to gain insights into their resistance mechanisms and transmission dynamics within the NICU.

METHODS: The study was conducted between November and December 2023 in a 5-bed NICU. Monthly surveillance cultures were performed to monitor colonization and infection with multidrug-resistant organisms. CRKP isolates were obtained from blood and nasal swabs of affected neonates. Identification and antimicrobial susceptibility testing were initially conducted using the Vitek[®]2 system with an N-395 card and further confirmed by 16S rRNA sequencing. Whole-genome sequencing (WGS) and antimicrobial resistance (AMR) profiling were performed to identify resistance genes and virulence factors. For genetic analysis, both Illumina short-read and Nanopore long-read sequencing were used, followed by hybrid assembly for enhanced genome resolution. Plasmid and resistance gene profiles were determined using AMRFinder and PlasmidFinder databases.

RESULTS: A total of three CRKP isolates (designated Kp1, Kp2, and Kp3) were identified. Kp1 and Kp2 belonged to sequence type (ST) ST23 and were genetically near-identical, differing by a single allele, while Kp3 was of a distinct sequence type, ST2096, with 245 allelic differences from Kp1 and Kp2. All isolates were resistant to colistin and carried resistance genes, including mcr-1 and bla NDM-1, bla KPC2 confirming carbapenem resistance. Efflux pump genes and aminoglycoside resistance genes were also detected, providing a multifaceted defence against antibiotics. Plasmid analysis identified several incompatibility groups (IncFI, IncHI, IncFIB, IncX), indicating the potential for horizontal gene transfer of resistance determinants.

CONCLUSION: This study highlights the complexity of CRKP outbreaks in neonatal care, with isolates exhibiting resistance mechanisms that complicate treatment. The plasmid profiles suggest these strains are reservoirs for multidrug-resistant genes, emphasizing the need for strict infection control and ongoing genomic surveillance. For neonatal care, these resistance challenges increase the risk of treatment failures and mortality, underscoring the importance of enhanced infection prevention and novel therapeutic strategies.},
}

Humans
*Klebsiella pneumoniae/genetics/drug effects/isolation & purification
*Klebsiella Infections/microbiology/epidemiology
*Cross Infection/microbiology
Infant, Newborn
*Colistin/pharmacology
*beta-Lactamases/genetics
*Anti-Bacterial Agents/pharmacology
*Whole Genome Sequencing
*Intensive Care Units, Neonatal
*Disease Outbreaks
*Genome, Bacterial/genetics
*Microbial Sensitivity Tests
Drug Resistance, Multiple, Bacterial/genetics
Plasmids/genetics
Neonatology
Bacterial Proteins/genetics
Carbapenem-Resistant Enterobacteriaceae/genetics/isolation & purification/drug effects
Male

@article {pmid39929813,
year = {2025},
author = {Liang, H and Xu, Y and Sahu, SK and Wang, H and Li, L and Chen, X and Zeng, Y and Lorenz, M and Friedl, T and Melkonian, B and Wong, GK and Melkonian, M and Liu, H and Wang, S},
title = {Chromosome-level genomes of two Bracteacoccaceae highlight adaptations to biocrusts.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1492},
pmid = {39929813},
issn = {2041-1723},
mesh = {*Gene Transfer, Horizontal ; Adaptation, Physiological/genetics ; Phylogeny ; Stress, Physiological/genetics ; Chromosomes/genetics ; },
abstract = {Biological soil crusts (biocrusts) cover the majority of the world's dryland ground and are a significant component of the vegetation-free surface of the planet. They consist of an intimate association of microbial organisms, lichens, bryophytes and fungi. Biocrusts are severely endangered by anthropogenic disturbances despite their importance. The genus Bracteacoccus (Sphaeropleales, Chlorophyta) is a ubiquitous component of biocrusts from extreme environments. Here, we present the chromosome-level genome sequences of two Bracteacoccus species, B. bullatus and B. minor. Genome comparisons with other Archaeplastida identify genomic features that highlight the adaptation of these algae to abiotic stresses prevailing in such environments. These features include horizontal gene transfer events mainly from bacteria or fungi, gains and expansions of stress-related gene families, neofunctionalization of genes following gene duplications and genome structural variations. We also summarize transcriptional and metabolic responses of the lipid pathway of B. minor, based on multi-omics analyses, which is important for balancing the flexible conversion of polar membrane lipids and non-polar storage lipids to cope with various abiotic stresses. Under dehydration and high-temperature stress conditions B. minor differs considerably from other eukaryotic algae. Overall, these findings provide insights into the genetic basis of adaptation to abiotic stress in biocrust algae.},
}

*Gene Transfer, Horizontal
Adaptation, Physiological/genetics
Phylogeny
Stress, Physiological/genetics
Chromosomes/genetics

@article {pmid39927357,
year = {2024},
author = {Al-Bukhalifa, MA and Al-Tameemi, HM},
title = {First whole genome sequencing of Staphylococcus aureus isolates from Iraq: Insights into zoonotic relations and biofilm-related genes.},
journal = {Open veterinary journal},
volume = {14},
number = {12},
pages = {3269-3288},
pmid = {39927357},
issn = {2218-6050},
mesh = {*Biofilms ; Animals ; *Staphylococcus aureus/genetics/isolation & purification/physiology ; Humans ; *Staphylococcal Infections/veterinary/microbiology ; *Whole Genome Sequencing ; Cats ; Iraq ; *Genome, Bacterial ; Dogs ; Cattle ; Sheep ; Zoonoses/microbiology ; },
abstract = {BACKGROUND: Staphylococcus aureus is a significant zoonotic pathogen capable of causing infections in both humans and animals. The bacterium's capacity to develop biofilms and resistance to many different antibiotics has raised significant concerns for public health. Furthermore, studies have demonstrated that horizontal gene transfer enables the transfer of deleterious features between strains found in humans and animals, consequently rendering treatment and control efforts more challenging.

AIM: This study aimed to investigate the relationships between human and animal isolates and biofilm-associated genes in local S. aureus strains using whole genome sequencing technique.

METHODS: We examined 111 suspected cases of S. aureus infection in humans and in animals and screened all S. aureus -positive isolates (11 isolates) for biofilm formation and antimicrobial profiles. Additionally, we sequenced and studied five S. aureus genomes isolated from humans, cows, sheep, cats, and dogs for significant biofilm-related genes and predicted their loci following annotation and deposition in the NCBI database.

RESULTS: The study showed that the isolates have genome sizes between 2.7 and 2.8 megabases, a GC content of 32.8%-33.1%, and a coding sequence count between 2,718 and 2,838. The cow isolate (MHB) and cat isolate (MHF) exhibited substantial genomic similarities with human isolates of S. aureus (N315) and the type strain of S. aureus (DSM 20231). The genomes of the human isolate (MHH) and the dog isolate (MHC) were comparable to S. aureus (N315). The sheep isolate (MHO) showed lesser genomic similarity and was closely related to S. aureus subsp. anaerobius. The genomes were submitted to the NCBI database with the following accession numbers: MHB (GCA_040196135.1), MHH (GCA_040196155.1), MHO (GCA_040195495.1), MHF (GCA_040195555.1), and MHC (GCA_040195445.1). The isolates were categorized by PubMLST typing into MHC (ST-1156), MHB (ST-6), MHF (ST-6), and MHO (a unique ST). We identified the accession numbers, locations, and lengths of biofilm-associated genes and regulators within the studied genomes.

CONCLUSION: The study is the first to conduct complete genome sequencing of Staphylococcus aureus in Iraq, allowing analysis of biofilm-associated genes in local isolates. It provides the first large-scale genomic investigation of genetic relationships among animal and human isolates in Iraq.},
}

*Biofilms
Animals
*Staphylococcus aureus/genetics/isolation & purification/physiology
Humans
*Staphylococcal Infections/veterinary/microbiology
*Whole Genome Sequencing
Cats
Iraq
*Genome, Bacterial
Dogs
Cattle
Sheep
Zoonoses/microbiology

@article {pmid39922005,
year = {2025},
author = {Iqbal, S and Begum, F and Manishimwe, C and Rabaan, AA and Sabour, AA and Alshiekheid, MA and Shaw, P},
title = {Allelochemicals degradation and multifarious plant growth promoting potential of two Bacillus spp.: Insights into genomic potential and abiotic stress alleviation.},
journal = {Chemosphere},
volume = {373},
number = {},
pages = {144191},
doi = {10.1016/j.chemosphere.2025.144191},
pmid = {39922005},
issn = {1879-1298},
abstract = {The deposition of allelochemicals poses a challenge to continuous cropping. Microbial degradation is an efficient approach to degrade these hazardous compounds. The current study employed an integrated approach to explore the allelochemical degradation potential of Bacillus subtilis RS10 and Bacillus pumilus SF-4 and concurrently validate their capabilities to enhance plant growth and alleviate abiotic stress in pot experiments. During initial in vitro screening, both strains utilized more than 45% of benzoic acid within 60 h of incubation and showed maximum growth after 72 h. Meanwhile, the wheat seed germination rate was increased by 34.33% and 30% when treated with strain RS10 and SF-4, respectively. In addition, both strains demonstrated the capacity to promote wheat growth in terms of root length, shoot length, and plant weight in soil contaminated with p-hydroxybenzoic acid. To determine the associated mechanism of plant growth-promoting and allelochemical degradation, the culture extract of RS10 and SF-4 were analyzed using gas chromatography-mass spectrometry, which showed several plant growth-promoting volatile organic compounds, including propanediol and butanone. Genome-wide analysis unveiled several genetic loci associated with plant growth-promoting traits such as siderophore synthesis, phosphate solubilization, and biosynthesis of biocontrol compounds. Moreover, the in-depth comparative genome analysis, horizontal gene transfer, and strain-specific genes unveiled intriguing insight into the evolutionary dynamics of these strains and constraints driven by natural selection. In conclusion, the current study revealed the multifarious plant growth-promoting traits of strains RS10 and SF-4 and suggested an application of these strains as plant growth stimulators in soil contaminated with allelochemicals.},
}

@article {pmid39921128,
year = {2025},
author = {Lavergne, JP and Page, A and Polard, P and Campo, N and Grangeasse, C},
title = {Quantitative phosphoproteomic reveals that the induction of competence modulates protein phosphorylation in Streptococcus pneumonaie.},
journal = {Journal of proteomics},
volume = {},
number = {},
pages = {105399},
doi = {10.1016/j.jprot.2025.105399},
pmid = {39921128},
issn = {1876-7737},
abstract = {Competence in the pathogenic bacterium Streptococcus pneumoniae (S. pneumoniae) is a developmental genetic program that is key for natural genetic transformation and consequently bacterial horizontal gene transfer. Phosphoproteomic studies have revealed that protein phosphorylation on serine, threonine and tyrosine residues is a widespread regulatory post-translational modification in bacteria. In this study, we performed quantitative proteomic and phosphoproteomic analyses on S. pneumoniae as a function of competence induction. To calculate peptide abundance ratios between non-competent and competent samples we used dimethyl-tag labeling. Titanium dioxide (TiO2) beads were used for phosphopeptide enrichment and samples were analysed by LC-MS/MS. Our proteome analysis covers approximatively 63 % of the total bacterial protein content, identifying 82 proteins with significantly different abundances ratios, including some not previously linked to competence. 248 phosphopeptides were identified including 47 having different abundance ratios. Notably, the proteins with a change in phosphorylation in competent cells are different from the proteins with a change in expression, highlighting different pathways induced by competence and regulated by phosphorylation. This is the first report that phosphorylation of some proteins is regulated during competence in Streptococcus pneumoniae, a key pathway for the bacteria to evade vaccines or acquire antibiotic resistance. SIGNIFICANCE: S. pneumoniae is a prominent model for the study of competence that governs the development of natural genetic transformation. The latter largely accounts for the spread of antibiotic resistance and vaccine evasion in pneumococcal isolates. Many proteins specifically expressed during competence have been identified and extensively studied. However, the potential contribution of post-translational modifications, and notably phosphorylation, during the development of competence has never been investigated. In this study, we used a quantitative phosphoproteomic approach to determine both the protein expression and the protein phosphorylation patterns. Comparison of these patterns allows to highlight a series of proteins that are differentially phosphorylated in the two conditions. This result opens new avenues to decipher new regulatory pathways induced by competence and that are potentially key for natural genetic transformation. Interfering with theses regulatory pathways could represent a promising strategy to combat antibiotic resistance in the future.},
}

@article {pmid39921114,
year = {2025},
author = {Farooq, S and Talat, A and Dhariwal, A and Petersen, FC and Khan, AU},
title = {Transgenerational Gut Dysbiosis: Unveiling the Dynamics of Antibiotic Resistance through Mobile Genetic Elements from Mothers to Infants.},
journal = {International journal of antimicrobial agents},
volume = {},
number = {},
pages = {107458},
doi = {10.1016/j.ijantimicag.2025.107458},
pmid = {39921114},
issn = {1872-7913},
abstract = {The initial microbial colonization of the gut is seeded by microbes transmitted from the mother's gut, skin, and vaginal tract. As the gut microbiome evolves, a few transmitted microbes persist throughout life. Understanding the impact of mother-to-neonate gut microbiome and antibiotic resistance genes (ARGs) transmission is crucial for establishing its role in infants' immunity against pathogens. This study primarily explores mother-neonate ARG transmission through 125 publicly available fecal metagenomes, isolated from eighteen mother-neonate pairs. The core ARGs, detected in both mothers and their respective infants at all stages (birth, 1[st], 2[nd], 3[rd], 4[th], 8[th] and 12[th] months) included aminoglycosidases APH(3')-IIIa, Bifidobacterium adolescentis rpoB mutants conferring resistance to rifampicin, β-lactamases CblA-1, CfxA2, multi-drug resistance gene CRP, diaminopyrimidine resistance gene dfrF, fluoroquinolone-resistance gene emrR, macrolide; lincosamide; streptogramin resistance gene ErmB, ErmG, macrolide resistance gene Mef(En2), nucleosidase SAT-4, and tetracycline-resistance genes tet(O), tet(Q), and tet(W). Most of these infants and mothers were not administered any antibiotics. In infants, ARGs were predominantly carried by Bacillota, Pseudomonadota, and Actinomycetota, similar to the mothers. The dominant ARG-carrying opportunistic pathogens were Escherichia coli, Klebsiella, and Streptococcus, found across all infant cohorts. All the core ARGs were associated with mobile genetic elements, signifying the role of horizontal gene transfer(HGT). We detected 132 virulence determinants, mostly Escherichia coli-specific, including pilus chaperones, general secretion pathway proteins, type III secretion system effectors, and heme-binding proteins. Maternal-neonate transmission of ARGs along with possible nosocomial infections, mode of delivery, breastfeeding versus formula feeding, and gestation period, must be considered for mother-neonate health.},
}

@article {pmid39918226,
year = {2025},
author = {Farfan, ABP and de Barrón, YLM and Yarihuamán, MMM and Príncipe Laines, FM and Paredes Pérez, MB and Choque, JSC and Pastor, HJB},
title = {Phylogenetic Analysis of Escherichia coli according to Phenotypic Resistance in Urinary Tract Infections in Children, Lima, Peru.},
journal = {Infection & chemotherapy},
volume = {},
number = {},
pages = {},
doi = {10.3947/ic.2024.0101},
pmid = {39918226},
issn = {2093-2340},
support = {A18010321/UNMSM/Universidad Nacional Mayor de San Marcos/Peru ; },
abstract = {BACKGROUND: Phylogenetic studies are essential for understanding the virulence and resistance factors of bacteria, especially in evaluating their distribution within specific populations for effective infection control. Urinary tract infections (UTIs) caused by Escherichia coli are highly prevalent and pose significant health challenges from childhood to adulthood. The rising incidence of multidrug-resistant (MDR) strains highlights the urgent need for research aimed at developing preventive measures and epidemiological control strategies. This study aimed to analyze phylogenetically uropathogenic E. coli strains and their resistance phenotypes in children.

MATERIALS AND METHODS: A retrospective analysis was conducted on 111 urine culture samples collected from June 2023 to February 2024 at the Pediatric Emergency Hospital (PEH) in Lima, Peru. The phylogroups of E. coli were identified using Clermont's protocol based on polymerase chain reaction.

RESULTS: UTIs were predominantly observed in females (85.6%) and infants under two years old (42.3%). The most frequent uropathogenic E. coli phylogroups were B2 (30.6%), D (29.7%), and A (25.2%). These phylogroups showed significant correlation with MDR and the production of extended spectrum beta-lactamases (ESBL).

CONCLUSION: At PEH, UTIs in children are primarily caused by uropathogenic E. coli from the B2 and D phylogroups, which demonstrate high virulence and resistance factors. The correlation between these phylogroups, MDR, and ESBL production, along with the increasing infection rates associated with phylogroup A, suggests a potential for horizontal gene transfer. This underscores the urgent need for vigilant control measures.},
}

@article {pmid39908756,
year = {2025},
author = {Xu, J and Ding, D and Fan, Y and Chen, R and Xia, Y and Liang, Y and Ding, Y and Feng, H},
title = {The overlooked risk of horizontal transfer of plasmid-borne antibiotic resistance genes induced by synthetic phenolic antioxidants.},
journal = {Journal of hazardous materials},
volume = {488},
number = {},
pages = {137459},
doi = {10.1016/j.jhazmat.2025.137459},
pmid = {39908756},
issn = {1873-3336},
abstract = {Plasmid-borne conjugation transfer of antibiotic resistance genes (ARGs) triggered by non-antibiotic stresses has attracted widespread attention, known to motivate conjugation through well-recognized reactive oxygen species and SOS response. However, a notable knowledge gap remains on the potential risks of reductive compounds, such as synthetic phenolic antioxidants (SPAs), in facilitating horizontal gene transfer by the other mechanisms beyond intracellular ROS. Therefore, intragenus and wastewater indigenous microbiota conjugation models were established to examine conjugative transfer frequency of RP4 plasmid under exposure of four extensively detected SPAs. The mechanisms were elucidated utilizing fluorescence detection, RT-qPCR, and transcriptomic analysis with 3-tert-butyl-4-hydroxyanisole (BHA) serving as a representative SPA. Results demonstrated that conjugation transfer frequencies of both models were significantly promoted without triggering SOS responses under exposure to high doses of BHA. Furthermore, BHA exposure benefited conjugation progress through improving membrane permeability of donors and ameliorating cellular energy supply. In addition, BHA exposure activated the RP4-encoded transfer apparatus by regulating the expression of associated genes. This study highlighted and provided a stark reminder about the potential horizontal gene transfer risks posed by SPAs exposure, which were regarded as a neglected driver in the dissemination of ARGs.},
}

@article {pmid39908303,
year = {2025},
author = {Poncin, K and McKeand, SA and Lavender, H and Kurzyp, K and Harrison, OB and Roberti, A and Melia, C and Johnson, E and Maiden, MCJ and Greaves, DR and Exley, R and Tang, CM},
title = {Bacteriocin-like peptides encoded by a horizontally acquired island mediate Neisseria gonorrhoeae autolysis.},
journal = {PLoS biology},
volume = {23},
number = {2},
pages = {e3003001},
pmid = {39908303},
issn = {1545-7885},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Neisseria gonorrhoeae/metabolism/genetics/pathogenicity/physiology ; *Bacteriocins/metabolism/genetics ; Humans ; *Gene Transfer, Horizontal ; Bacteriolysis ; Genomic Islands ; Gonorrhea/microbiology ; },
abstract = {Neisseria gonorrhoeae is a human-specific pathogen that causes the important sexually transmitted infection, gonorrhoea, an inflammatory condition of the genitourinary tract. The bacterium is closely related to the meningococcus, a leading cause of bacterial meningitis. Both these invasive bacterial species undergo autolysis when in the stationary phase of growth. Autolysis is a form of programmed cell death (PCD) which is part of the life cycle of remarkably few bacteria and poses an evolutionary conundrum as altruistic death provides no obvious benefit for single-celled organisms. Here, we searched for genes present in these 2 invasive species but not in other members of the Neisseria genus. We identified a ~3.4 kb horizontally acquired region, we termed the nap island, which is largely restricted to the gonococcus and meningococcus. The nap island in the gonococcus encodes 3 cationic, bacteriocin-like peptides which have no detectable antimicrobial activity. Instead, the gonococcal Neisseria autolysis peptides (Naps) promote autolytic cell death when bacteria enter the stationary phase of growth. Furthermore, strains lacking the Naps exhibit reduced autolysis in assays of PCD. Expression of Naps is likely to be phase variable, explaining how PCD could have arisen in these important human pathogens. NapC also induces lysis of human cells, so the peptides are likely to have multiple roles during colonisation and disease. The acquisition of the nap island contributed to the emergence of PCD in the gonococcus and meningococcus and potentially to the appearance of invasive disease in Neisseria spp.},
}

*Neisseria gonorrhoeae/metabolism/genetics/pathogenicity/physiology
*Bacteriocins/metabolism/genetics
Humans
*Gene Transfer, Horizontal
Bacteriolysis
Genomic Islands
Gonorrhea/microbiology

@article {pmid39907470,
year = {2025},
author = {Wang, X and Koster, Ad and Koenders, BB and Jonker, M and Brul, S and Ter Kuile, BH},
title = {De novo acquisition of antibiotic resistance in six species of bacteria.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0178524},
doi = {10.1128/spectrum.01785-24},
pmid = {39907470},
issn = {2165-0497},
abstract = {Bacteria can become resistant to antibiotics in two ways: by acquiring resistance genes through horizontal gene transfer and by de novo development of resistance upon exposure to non-lethal concentrations. The importance of the second process, de novo build-up, has not been investigated systematically over a range of species and may be underestimated as a result. To investigate the DNA mutation patterns accompanying the de novo antibiotic resistance acquisition process, six bacterial species encountered in the food chain were exposed to step-wise increasing sublethal concentrations of six antibiotics to develop high levels of resistance. Phenotypic and mutational landscapes were constructed based on whole-genome sequencing at two time points of the evolutionary trajectory. In this study, we found that (1) all of the six strains can develop high levels of resistance against most antibiotics; (2) increased resistance is accompanied by different mutations for each bacterium-antibiotic combination; (3) the number of mutations varies widely, with Y. enterocolitica having by far the most; (4) in the case of fluoroquinolone resistance, a mutational pattern of gyrA combined with parC is conserved in five of six species; and (5) mutations in genes coding for efflux pumps are widely encountered in gram-negative species. The overall conclusion is that very similar phenotypic outcomes are instigated by very different genetic changes. The outcome of this study may assist policymakers when formulating practical strategies to prevent development of antimicrobial resistance in human and veterinary health care.IMPORTANCEMost studies on de novo development of antimicrobial resistance have been performed on Escherichia coli. To examine whether the conclusions of this research can be applied to more bacterial species, six species of veterinary importance were made resistant to six antibiotics, each of a different class. The rapid build-up of resistance observed in all six species upon exposure to non-lethal concentrations of antimicrobials indicates a similar ability to adjust to the presence of antibiotics. The large differences in the number of DNA mutations accompanying de novo resistance suggest that the mechanisms and pathways involved may differ. Hence, very similar phenotypes can be the result of various genotypes. The implications of the outcome are to be considered by policymakers in the area of veterinary and human healthcare.},
}

@article {pmid39904308,
year = {2025},
author = {Whiteman, NK},
title = {Insect herbivory: An inordinate fondness for plant cell wall degrading enzymes.},
journal = {Current biology : CB},
volume = {35},
number = {3},
pages = {R107-R109},
doi = {10.1016/j.cub.2024.12.045},
pmid = {39904308},
issn = {1879-0445},
mesh = {Animals ; *Cell Wall/metabolism ; *Herbivory ; Coleoptera/physiology/genetics/enzymology ; Symbiosis ; Plants ; Gene Transfer, Horizontal ; },
abstract = {Tens of thousands of species of leaf beetles rely on plant cell wall degrading enzymes in order to make the most of nutritionally depauperate plant tissues. Many of the genes encoding these enzymes were acquired from microbial donors, either through horizontal gene transfer or by hosting microbial endosymbionts. A new study explores how these insects have leveraged this metabolic potential to diversify and expand into new niches.},
}

Animals
*Cell Wall/metabolism
*Herbivory
Coleoptera/physiology/genetics/enzymology
Symbiosis
Plants
Gene Transfer, Horizontal

@article {pmid39902196,
year = {2024},
author = {Chen, R and Rao, R and Wang, C and Zhu, D and Yuan, F and Yue, L},
title = {Features and evolutionary adaptations of the mitochondrial genome of Garuga forrestii W. W. Sm.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1509669},
pmid = {39902196},
issn = {1664-462X},
abstract = {INTRODUCTION: Garuga forrestii W. W. Sm. is a tree species of the Burseraceae family, endemic to China, found in hot/warm-dry valleys. This species plays a crucial role in maintaining biodiversity in these ecosystems.

METHODS: We performed de novo assembly of the Garuga forrestii mitochondrial genome using PMAT (v.1.5.4), resulting in a typical circular molecule of 606,853 bp. The genome consists of 31 tRNA genes, 3 rRNA genes, 35 protein-coding genes, and 1 pseudogene. The study also investigates RNA editing sites and evolutionary patterns.

RESULTS: The mitochondrial genome exhibits a low proportion of repetitive sequences (3.30%), suggesting a highly conserved structure. A high copy number of the trnM-CAT gene (4 copies) is noted, which may contribute to genomic rearrangement and adaptive evolution. Among the 476 RNA editing sites, hydrophilic-hydrophobic and hydrophobic-hydrophobic editing events are most common, accounting for 77.10%. Negative selection predominates among most genes (Ka/Ks < 1), while a few genes (e.g., matR, nad3, rps1, rps12, and rps4) show signs of positive selection (Ka/Ks > 1), potentially conferring evolutionary advantages. Additionally, a significant A/T bias is observed at the third codon position. Phylogenomic analysis supports the APG IV classification, with no evidence of horizontal gene transfer.

DISCUSSION: This mitochondrial genome offers valuable insights into the adaptive mechanisms and evolutionary processes of Garuga forrestii. It enhances our understanding of the species' biogeography in tropical Southeast Asia and Southwest China, providing key information on the evolutionary history of this genus.},
}

@article {pmid39902180,
year = {2024},
author = {Li, X and Zhu, Y and Lu, Y and Wu, K and Che, Y and Wang, X and Wang, W and Gao, J and Gao, J and Liu, Z and Zhou, Z},
title = {Population genetic analysis of clinical Mycobacterium abscessus complex strains in China.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1496896},
pmid = {39902180},
issn = {2235-2988},
mesh = {China ; *Mycobacterium abscessus/genetics/drug effects/classification/isolation & purification ; Humans ; *Multilocus Sequence Typing ; *Genome, Bacterial ; *Mycobacterium Infections, Nontuberculous/microbiology/epidemiology ; *Virulence Factors/genetics ; Anti-Bacterial Agents/pharmacology ; Genetic Variation ; Phylogeny ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; Genetics, Population ; },
abstract = {BACKGROUND: To explore the genetic characteristics of the Mycobacterium abscessus complex (MABC) population in China, given its rising clinical importance among nontuberculous mycobacteria.

METHODS: We conducted population genetic analyses on 360 MABC genomes from China, focusing on core genome multilocus sequence typing (cgMLST), pan-genome characterization, population genetics, and antimicrobial resistance gene profiling.

RESULTS: Our analysis identified 273 M. abscessus subsp. abscessus (MabA) and 87 M. abscessus subsp. massiliense (MabM) isolates, uncovering 68 sequence types (STs), with ST5 being the most common. cgMLST classified 33.3% of isolates into six dominant circulating clones (DCCs) and 49.4% into 59 genomic clusters at a threshold of 25 different alleles, including 18 international clusters linking Chinese isolates with seven other countries. The MABC pan-genome is open, with MabA exhibiting greater accessory gene diversity and higher gene turnover compared to MabM. Mobile genetic elements (MGEs), such as prophages and genomic islands, were prevalent across all genomes. 139 to 151 virulence factors (VFs) were identified per genome, with distinct accessory VFs in MabA and MabM affecting immune modulation and metabolism. Resistance gene profiling revealed ubiquitous mtrA, RbpA, and bla MAB, with MabA-specific erm(41) conferring resistance to macrolides and β-lactams. Common rrs and rrl gene mutations indicated widespread resistance to aminoglycosides and macrolides, while gyrA mutations suggested emerging fluoroquinolone resistance. An acquired erm(46) gene, likely obtained via phage-mediated horizontal gene transfer, was detected in one MabA strain.

CONCLUSION: This study provides key genetic insights into the dynamics of MABC in China. The widespread distribution of DCCs, high genomic clustering rates, open pan-genome, and distinct resistance patterns between MabA and MabM, along with MGEs, highlight the need for targeted surveillance and tailored therapies to address emerging challenges in MABC infections.},
}

China
*Mycobacterium abscessus/genetics/drug effects/classification/isolation & purification
Humans
*Multilocus Sequence Typing
*Genome, Bacterial
*Mycobacterium Infections, Nontuberculous/microbiology/epidemiology
*Virulence Factors/genetics
Anti-Bacterial Agents/pharmacology
Genetic Variation
Phylogeny
Drug Resistance, Bacterial/genetics
Microbial Sensitivity Tests
Genetics, Population

@article {pmid39901063,
year = {2025},
author = {Wiśniewska, MM and Kyslík, J and Alama-Bermejo, G and Lövy, A and Kolísko, M and Holzer, AS and Kosakyan, A},
title = {Comparative transcriptomics reveal stage-dependent parasitic adaptations in the myxozoan Sphaerospora molnari.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {103},
pmid = {39901063},
issn = {1471-2164},
support = {19-25536Y//Grantová Agentura České Republiky/ ; 19-28399X//Grantová Agentura České Republiky/ ; 20-30321Y//Grantová Agentura České Republiky/ ; CZ.02.1.01/0.0/0.0/16_019/0000759//ERD fund Centre for Research of Pathogenicity and Virulence Parasites/ ; },
mesh = {*Myxozoa/genetics/pathogenicity/physiology ; Animals ; *Transcriptome ; Gene Expression Profiling ; Host-Parasite Interactions/genetics ; Adaptation, Physiological/genetics ; Gills/parasitology ; Carps/parasitology ; Fish Diseases/parasitology ; Life Cycle Stages/genetics ; },
abstract = {BACKGROUND: Parasitism as a life strategy has independently evolved multiple times within the eukaryotic tree of life. Each lineage has developed mechanisms to invade hosts, exploit resources, and ensure replication, but our knowledge of survival mechanisms in many parasitic taxa remain extremely limited. One such group is the Myxozoa, which are obligate, dixenous cnidarians. Evidence suggests that myxozoans evolved from free-living ancestors to endoparasites around 600 million years ago and are likely one of the first metazoan parasites on Earth. Some myxozoans pose significant threats to farmed and wild fish populations, negatively impacting aquaculture and fish stocks; one such example is Sphaerospora molnari, which forms spores in the gills of common carp (Cyprinus carpio), disrupting gill epithelia and causing somatic and respiratory failure. Sphaerospora molnari undergoes sequential development in different organs of its host, with large numbers of morphologically distinct stages occurring in the blood, liver, and gills of carp. We hypothesize that these parasite life-stages differ in regards to their host exploitation, pathogenicity, and host immune evasion strategies and mechanisms. We performed stage-specific transcriptomic profiling to identify differentially expressed key functional gene groups that relate to these functions and provide a fundamental understanding of the mechanisms S. molnari uses to optimize its parasitic lifestyle. We aimed to identify genes that are likely related to parasite pathogenicity and host cell exploitation mechanisms, and we hypothesize that genes unique to S. molnari might be indicative of evolutionary innovations and specific adaptations to host environments.

RESULTS: We used parasite isolation protocols and comparative transcriptomics to study early proliferative and spore-forming stages of S. molnari, unveiling variation in gene expression between each stage. We discovered several apparent innovations in the S. molnari transcriptome, including proteins that are likely to function in the uptake of previously unknown key nutrients, immune evasion factors that may contribute to long-term survival in hosts, and proteins that likely improve adhesion to host cells that may have arisen from horizontal gene transfer. Notably, we identified genes that are similar to known virulence factors in other parasitic organisms, particularly blood and intestinal parasites like Plasmodium, Trypanosoma, and Giardia. Many of these genes are absent in published cnidarian and myxozoan datasets and appear to be specific to S. molnari; they may therefore represent potential innovations enabling Sphaerospora to exploit the host's blood system.

CONCLUSIONS: In order to address the threat posed by myxozoans to both cultured fish species and wild stocks, it is imperative to deepen our understanding of their genetics. Sphaerospora molnari offers an appealing model for stage-specific transcriptomic profiling and for identifying differentially expressed key functional gene groups related to parasite development. We identified genes that are thus far unique to S. molnari, which reveal their evolutionary novelty and likely role as adaptations to specific host niches. In addition, we describe the pathogenicity-associated genetic toolbox of S. molnari and discuss the implications of our discoveries for disease control by shedding light on specific targets for potential intervention strategies.},
}

*Myxozoa/genetics/pathogenicity/physiology
Animals
*Transcriptome
Gene Expression Profiling
Host-Parasite Interactions/genetics
Adaptation, Physiological/genetics
Gills/parasitology
Carps/parasitology
Fish Diseases/parasitology
Life Cycle Stages/genetics

@article {pmid39900484,
year = {2025},
author = {Van Etten, J and Stephens, TG and Bhattacharya, D},
title = {Genetic Transfer in Action: Uncovering DNA Flow in an Extremophilic Microbial Community.},
journal = {Environmental microbiology},
volume = {27},
number = {2},
pages = {e70048},
pmid = {39900484},
issn = {1462-2920},
support = {//U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231/ ; 10.46936/10.25585/60000481//Joint Genome Institute/ ; NJ01180//National Institute of Food and Agriculture/ ; 80NSSC19K1542/NASA/NASA/United States ; NASA (80NSSC19K0462)/NASA/NASA/United States ; },
mesh = {*Gene Transfer, Horizontal ; *Bacteria/genetics/classification ; Extremophiles/genetics ; Microbiota/genetics ; DNA, Bacterial/genetics ; Genome, Bacterial ; },
abstract = {Horizontal genetic transfer (HGT) is a significant driver of genomic novelty in all domains of life. HGT has been investigated in many studies however, the focus has been on conspicuous protein-coding DNA transfers that often prove to be adaptive in recipient organisms and are therefore fixed longer-term in lineages. These results comprise a subclass of HGTs and do not represent exhaustive (coding and non-coding) DNA transfer and its impact on ecology. Uncovering exhaustive HGT can provide key insights into the connectivity of genomes in communities and how these transfers may occur. In this study, we use the term frequency-inverse document frequency (TF-IDF) technique, that has been used successfully to mine DNA transfers within real and simulated high-quality prokaryote genomes, to search for exhaustive HGTs within an extremophilic microbial community. We establish a pipeline for validating transfers identified using this approach. We find that most DNA transfers are within-domain and involve non-coding DNA. A relatively high proportion of the predicted protein-coding HGTs appear to encode transposase activity, restriction-modification system components, and biofilm formation functions. Our study demonstrates the utility of the TF-IDF approach for HGT detection and provides insights into the mechanisms of recent DNA transfer.},
}

*Gene Transfer, Horizontal
*Bacteria/genetics/classification
Extremophiles/genetics
Microbiota/genetics
DNA, Bacterial/genetics
Genome, Bacterial

@article {pmid39897699,
year = {2025},
author = {Theobald, S and Vesth, T and Nybo, JL and Frisvad, JC and Kjærbølling, I and Mondo, S and LaButti, K and Haridas, S and Riley, R and Kuo, AA and Salamov, AA and Pangilinan, J and Lipzen, A and Koriabine, M and Yan, M and Barry, K and Clum, A and Lyhne, EK and Drula, E and Wiebenga, A and Müller, A and Lubbers, RJM and Kun, RS and Dos Santos Gomes, AC and Mäkelä, MR and Henrissat, B and Simmons, BA and Magnuson, JK and Hoof, JB and Mortensen, UH and Dyer, PS and Momany, M and Larsen, TO and Grigoriev, IV and Baker, SE and de Vries, RP and Andersen, MR},
title = {Comparative genomics of Aspergillus nidulans and section Nidulantes.},
journal = {Current research in microbial sciences},
volume = {8},
number = {},
pages = {100342},
pmid = {39897699},
issn = {2666-5174},
abstract = {Aspergillus nidulans is an important model organism for eukaryotic biology and the reference for the section Nidulantes in comparative studies. In this study, we de novo sequenced the genomes of 25 species of this section. Whole-genome phylogeny of 34 Aspergillus species and Penicillium chrysogenum clarifies the position of clades inside section Nidulantes. Comparative genomics reveals a high genetic diversity between species with 684 up to 2433 unique protein families. Furthermore, we categorized 2118 secondary metabolite gene clusters (SMGC) into 603 families across Aspergilli, with at least 40 % of the families shared between Nidulantes species. Genetic dereplication of SMGC and subsequent synteny analysis provides evidence for horizontal gene transfer of a SMGC. Proteins that have been investigated in A. nidulans as well as its SMGC families are generally present in the section Nidulantes, supporting its role as model organism. The set of genes encoding plant biomass-related CAZymes is highly conserved in section Nidulantes, while there is remarkable diversity of organization of MAT-loci both within and between the different clades. This study provides a deeper understanding of the genomic conservation and diversity of this section and supports the position of A. nidulans as a reference species for cell biology.},
}

@article {pmid39894155,
year = {2025},
author = {Ren, B and Shi, X and Guo, J and Jin, P},
title = {Interaction of sulfate-reducing bacteria and methanogenic archaea in urban sewers, leads to increased risk of proliferation of antibiotic resistance genes.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {125777},
doi = {10.1016/j.envpol.2025.125777},
pmid = {39894155},
issn = {1873-6424},
abstract = {Sewers are considered a potential reservoir of antibiotic resistance. However, the generation of antibiotic resistance genes (ARGs) in microbial communities in pipeline biofilms under antibiotic stress remains unexplored. In this study, the biodegradation efficiency of tetracycline (TCY) and sulfamethoxazole (SMX) was evaluated in a pilot reactor of the sewers. The results showed that under TCY and SMX stress, the degradation efficiency of sewage water was inhibited. The most abundant ARGs detected in the biofilm samples were TCY-related genes (e.g., tetW/N/W, tetC, and tetM), accounting for 34.1%. The microbial community composition varied, and the correlation analysis showed that antibiotic stress had a certain impact on the biological metabolic activity and function of the urban sewers. The community structure and diversity of biofilms enabled the evaluation of the bioconversion of antibiotics. Notably, Anaerocella and Paludibacter directly influenced the methanogenesis and sulfate reduction processes, playing a key role in the interaction between sulfate-reducing bacteria and methanogenic archaea. These microorganisms facilitated the proliferation of ARGs (tet and sul) in the biofilms through horizontal gene transfer. This study provides insight into the front-end control of ARGs, further improving sewage treatment plant processes and reducing the environmental and health risks caused by antibiotic abuse.},
}

@article {pmid39718247,
year = {2025},
author = {Santos, PKF and de Souza Araujo, N and Françoso, E and Werren, JH and Kapheim, KM and Arias, MC},
title = {The genome of the solitary bee Tetrapedia diversipes (Hymenoptera, Apidae).},
journal = {G3 (Bethesda, Md.)},
volume = {15},
number = {2},
pages = {},
doi = {10.1093/g3journal/jkae264},
pmid = {39718247},
issn = {2160-1836},
support = {001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 306932/2016-4//CNPq - Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 2013/12530-4//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; DEB1257053//USNSF/ ; },
mesh = {Animals ; Bees/genetics/microbiology ; *Genome, Insect ; Molecular Sequence Annotation ; Genomics/methods ; Wolbachia/genetics ; Phylogeny ; DNA Transposable Elements ; Gene Transfer, Horizontal ; Symbiosis/genetics ; },
abstract = {Tetrapedia diversipes is a Neotropical solitary bee commonly found in trap-nests, known for its morphological adaptations for floral oil collection and prepupal diapause during the cold and dry season. Here, we present the genome assembly of T. diversipes (332 Mbp), comprising 2,575 scaffolds, with 15,028 predicted protein-coding genes. Repetitive elements constitute 38.68% of the genome, notably Class II transposable elements. An investigation into lateral gene transfers identified a low frequency (0.037%) of nuclear copies of mitochondrial DNA and 18 candidate regions from bacterial origins. Furthermore, the annotation of 3 scaffolds reveals the presence of the Wolbachia endosymbiont genome, confirming the infection by 2 strains in T. diversipes populations. This genome contributes valuable insights into Neotropical bee genomics, offering a resource for comparative studies and enhancing our understanding of the molecular basis of solitary bee adaptations and interactions.},
}

Animals
Bees/genetics/microbiology
*Genome, Insect
Molecular Sequence Annotation
Genomics/methods
Wolbachia/genetics
Phylogeny
DNA Transposable Elements
Gene Transfer, Horizontal
Symbiosis/genetics

@article {pmid39883727,
year = {2025},
author = {Wielert, I and Kraus-Römer, S and Volkmann, TE and Craig, L and Higgins, PG and Maier, B},
title = {Pilin antigenic variants impact gonococcal lifestyle and antibiotic tolerance by modulating interbacterial forces.},
journal = {PLoS biology},
volume = {23},
number = {1},
pages = {e3003022},
doi = {10.1371/journal.pbio.3003022},
pmid = {39883727},
issn = {1545-7885},
abstract = {Type 4 pili (T4P) are multifunctional filaments involved in adhesion, surface motility, biofilm formation, and horizontal gene transfer. These extracellular polymers are surface-exposed and, therefore, act as antigens. The human pathogen Neisseria gonorrhoeae uses pilin antigenic variation to escape immune surveillance, yet it is unclear how antigenic variation impacts most other functions of T4P. Here, we addressed this question by replacing the major pilin of a laboratory strain with pilins from clinical isolates. We reveal that the resulting strains vary substantially in their attractive forces. Strongly interacting bacteria form microcolonies while weakly interacting bacteria retain a planktonic lifestyle. In mixed microcolonies, different variant strains segregate in agreement with the differential strength of adhesion hypothesis. By combining structural predictions and laser tweezers experiments, we show that the C-terminal region of the pilin is crucial for attraction. Lifestyle affects growth kinetics and antibiotic tolerance. In the presence of ceftriaxone or ciprofloxacin, the killing kinetics indicate strongly increased tolerance of aggregating strains. We propose that pilin antigenic variation produces a mixed population containing variants optimized for growth, colonization, or survivability under external stress. Different environments select different variants, ensuring the survival and reproduction of the population as a whole.},
}

@article {pmid39882964,
year = {2025},
author = {Warren, JM and Ceriotti, LF and Sanchez-Puerta, MV and Sloan, DB},
title = {Fungal-derived tRNAs are expressed and aminoacylated in orchid mitochondria.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf025},
pmid = {39882964},
issn = {1537-1719},
abstract = {Plant mitochondrial genomes (mitogenomes) experience remarkable levels of horizontal gene transfer (HGT), including the recent discovery that orchids anciently acquired DNA from fungal mitogenomes. Thus far, however, there is no evidence that any of the genes from this interkingdom HGT are functional in orchid mitogenomes. Here, we applied a specialized sequencing approach to the orchid Corallorhiza maculata and found that some fungal-derived tRNA genes in the transferred region are transcribed, post-transcriptionally modified, and aminoacylated. In contrast, all the transferred protein-coding sequences appear to be pseudogenes. These findings show that fungal HGT has altered the composition of the orchid mitochondrial tRNA pool and suggest that these foreign tRNAs function in translation. The exceptional capacity of tRNAs for HGT and functional replacement is further illustrated by the diversity of tRNA genes in the C. maculata mitogenome, which also include genes of plastid and bacterial origin in addition to their native mitochondrial counterparts.},
}

@article {pmid39881475,
year = {2025},
author = {Wang, P and Wang, H and Qi, S and Wang, W and Lu, H},
title = {Synergistic effects of quaternary ammonium compounds and antibiotics on the evolution of antibiotic resistance.},
journal = {Water research},
volume = {275},
number = {},
pages = {123206},
doi = {10.1016/j.watres.2025.123206},
pmid = {39881475},
issn = {1879-2448},
abstract = {The usage of quaternary ammonium compounds (QACs) as disinfectants has surged dramatically during the COVID-19 pandemic and thereafter. QACs can promote antimicrobial resistance, but the combined effects of QACs and antibiotics in driving resistance evolution were yet revealed. This study aimed to evaluate antibiotic resistance of wastewater microorganisms under coexposure to typical antibiotics and the most widely used QAC, dodecyl dimethyl benzyl ammonium chloride (DDBAC). DDBAC exhibited synergistic effects with multiple antibiotics (ampicillin, azithromycin, ciprofloxacin, kanamycin, polymyxin B) in enhancing activated sludge resistance by 1.53-6.67 folds, compared with antibiotics exposure alone. DDBAC-ampicillin coexposure enriched multidrug and aminoglycoside ARGs with relatively high horizontal gene transfer potential. The synergistic mechanism was further explored using sludge-isolated pathogenic E. coli. DDBAC at 1-10 mg/L alone did not induce notable resistance, but synergized with ampicillin on enhancing resistance by 6.56-22.90 folds. Based on mutation analysis and transcriptomics, DDBAC-enhanced resistance evolution was attributable to efflux pump upregulation, target modification, and inhibition of ATP synthesis (a less reported mechanism). Five DDBAC-induced, resistance-conferring mutant genes were highly enriched in globally collected E. coli strains from wastewater outflow (n = 537) than soil/sediments (n = 714, p < 0.05). Considering the strong adsorption and persistence of QACs, their coexistence with antibiotics poses elevated antimicrobial resistance risks, particularly in wastewater treatment systems with long solid retention time and sewage sludge applied farmland.},
}

@article {pmid39688393,
year = {2025},
author = {Lurie-Weinberger, MN and Bychenko-Banyas, D and Mor, M and Laviad-Shitrit, S and Kaplan, E and Rakovitsky, N and Keren-Paz, A and Ben-Zvi, C and Carmeli, Y},
title = {In vivo interspecies dissemination of IncM2-type blaNDM-1 carrying plasmid.},
journal = {Microbiology spectrum},
volume = {13},
number = {2},
pages = {e0039924},
doi = {10.1128/spectrum.00399-24},
pmid = {39688393},
issn = {2165-0497},
mesh = {*beta-Lactamases/genetics/metabolism ; *Plasmids/genetics ; *Klebsiella pneumoniae/genetics/drug effects ; Humans ; *Drug Resistance, Multiple, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; *Escherichia coli/genetics/drug effects ; Klebsiella Infections/microbiology ; Bacterial Proteins/genetics/metabolism ; Microbial Sensitivity Tests ; Gene Transfer, Horizontal ; Male ; Whole Genome Sequencing ; Escherichia coli Infections/microbiology ; Female ; Aged ; },
abstract = {The gastrointestinal tract is a unique ecological niche with a high abundance of various Enterobacterales in close proximity. This allows the exchange of mobile genetic elements that carry resistance determinants. In the hospital setting, resistant organisms are prevalent and selective antibiotic pressure is high, providing a supportive platform for interspecies dissemination of resistance. Seven New Delhi metallo-beta-lactamase(NDM) positive and one NDM-negative bacteria were sent for WGS followed by bioinformatics analysis. Here, we describe three separate cases of patients simultaneously colonized by two NDM producing-species (Escherichia coli and Klebsiella pneumoniae), in which we documented interspecies dissemination of the blaNDM-1 by an 87,450 bp IncM2 type multi-drug resistance plasmid (here named pNCICAN_NDM-01_21-il). This plasmid was found to be highly conjugative. Our results underline the risk of interspecies horizontal plasmid dissemination. Such events may cause the emergence of high-risk clones, as well as lead to under-recognized multi-species outbreaks.IMPORTANCEConjugative, carbapenemase-carrying multidrug-resistant plasmids that can move between species of clinically relevant Enterobacterales pose a great risk to patients' health, especially when they spread inside a medical institution. Yet, most institutions monitor bacteria according to species and are at risk of missing plasmid-driven outbreaks. Thus, this work indicates that plasmid surveillance is an important tool for infection control.},
}

*beta-Lactamases/genetics/metabolism
*Plasmids/genetics
*Klebsiella pneumoniae/genetics/drug effects
Humans
*Drug Resistance, Multiple, Bacterial/genetics
*Anti-Bacterial Agents/pharmacology
*Escherichia coli/genetics/drug effects
Klebsiella Infections/microbiology
Bacterial Proteins/genetics/metabolism
Microbial Sensitivity Tests
Gene Transfer, Horizontal
Male
Whole Genome Sequencing
Escherichia coli Infections/microbiology
Female
Aged

@article {pmid39880121,
year = {2025},
author = {Almeida-Santos, AC and Novais, C and Peixe, L and Freitas, AR},
title = {Vancomycin-Resistant Enterococcus faecium: A current perspective on resilience, adaptation, and the urgent need for novel strategies.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2025.01.016},
pmid = {39880121},
issn = {2213-7173},
abstract = {Vancomycin-resistant Enterococcus faecium (VREfm) has become a critical opportunistic pathogen, urgently requiring new antimicrobial strategies due to its rising prevalence and significant impact on patient safety and healthcare costs. VREfm continues to evolve through mutations and the acquisition of new genes via horizontal gene transfer, contributing to resistance against several last-resort antibiotics. Although primarily hospital-associated, VREfm is also detected in the community, food chain, livestock, and environmental sources like wastewater, indicating diverse transmission pathways and the need for a One Health approach. Advances in genomics have shed light on VREfm's persistence in hospital settings, particularly its adaptation to the gastrointestinal tract of hospitalized patients, recent clonal shifts, and the dominance of specific clonal lineages. Despite extensive research, significant gaps remain in understanding the molecular mechanisms behind VREfm's unique adaptation to clinical environments. In this review, we aim to present an overview of VREfm current prevalence, mechanisms of resistance, and unveil the adaptive traits that have facilitated VREfm's rise and global success. A particular focus is given to key plasmids, namely linear plasmids, virulence factors, and bacteriocins as potential drivers in the global emergence of the ST78 clonal lineage. We also address diagnostic challenges and the limited treatment options available for VREfm, as well as emerging antibiotic alternatives aimed at restoring gut microbiota balance and curbing VREfm proliferation. A multifaceted approach combining research, clinical practices, and public health policies is crucial to mitigate the impact of this superbug and preserve antimicrobial effectiveness for future generations.},
}

@article {pmid39878503,
year = {2025},
author = {Ndovie, W and Havránek, J and Leconte, J and Koszucki, J and Chindelevitch, L and Adriaenssens, EM and Mostowy, RJ},
title = {Exploration of the genetic landscape of bacterial dsDNA viruses reveals an ANI gap amid extensive mosaicism.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0166124},
doi = {10.1128/msystems.01661-24},
pmid = {39878503},
issn = {2379-5077},
abstract = {Average nucleotide identity (ANI) is a widely used metric to estimate genetic relatedness, especially in microbial species delineation. While ANI calculation has been well optimized for bacteria and closely related viral genomes, accurate estimation of ANI below 80%, particularly in large reference data sets, has been challenging due to a lack of accurate and scalable methods. To bridge this gap, we introduce MANIAC, an efficient computational pipeline optimized for estimating ANI and alignment fraction (AF) in viral genomes with divergence around ANI of 70%. Using a rigorous simulation framework, we demonstrate MANIAC's accuracy and scalability compared to existing approaches, even to data sets of hundreds of thousands of viral genomes. Applying MANIAC to a curated data set of complete bacterial dsDNA viruses revealed a multimodal ANI distribution, with a distinct gap around 80%, akin to the bacterial ANI gap (~90%) but shifted, likely due to viral-specific evolutionary processes such as recombination dynamics and mosaicism. We then evaluated ANI and AF as predictors of genus-level taxonomy using a logistic regression model. We found that this model has strong predictive power (PR-AUC = 0.981), but that it works much better for virulent (PR-AUC = 0.997) than temperate (PR-AUC = 0.847) bacterial viruses. This highlights the complexity of taxonomic classification in temperate phages, known for their extensive mosaicism, and cautions against over-reliance on ANI in such cases. MANIAC can be accessed at https://github.com/bioinf-mcb/MANIAC.IMPORTANCEWe introduce a novel computational pipeline called MANIAC, designed to accurately assess average nucleotide identity (ANI) and alignment fraction (AF) between diverse viral genomes, scalable to data sets of over 100k genomes. Using computer simulations and real data analyses, we show that MANIAC could accurately estimate genetic relatedness between pairs of viral genomes of around 60%-70% ANI. We applied MANIAC to investigate the question of ANI discontinuity in bacterial dsDNA viruses, finding evidence for an ANI gap, akin to the one seen in bacteria but around ANI of 80%. We then assessed the ability of ANI and AF to predict taxonomic genus boundaries, finding its strong predictive power in virulent, but not in temperate phages. Our results suggest that bacterial dsDNA viruses may exhibit an ANI threshold (on average around 80%) above which recombination helps maintain population cohesiveness, as previously argued in bacteria.},
}